4HJH | pdb_00004hjh

Iodide SAD phased crystal structure of a phosphoglucomutase from Brucella melitensis complexed with glucose-6-phosphate

PDB DOI: https://doi.org/10.2210/pdb4HJH/pdb

Classification: ISOMERASE
Organism(s): Brucella melitensis bv. 1 str. 16M
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-10-12 Released: 2012-11-21
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.209 (Depositor), 0.210 (DCC)
R-Value Work:
0.174 (Depositor), 0.181 (DCC)
R-Value Observed:
0.175 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Iodide SAD phased crystal structure of a phosphoglucomutase from Brucella melitensis complexed with glucose-6-phosphate

Fairman, J.W., Craig, T.K., Staker, B.L.

To be published.

Macromolecule Content

Total Structure Weight: 112.67 kDa
Atom Count: 7,469
Modeled Residue Count: 931
Deposited Residue Count: 962
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphomannomutase	A, B	481	Brucella melitensis bv. 1 str. 16M	Mutation(s): 0 Gene Names: BAWG_1686 EC: 5.4.2.8
UniProt
Find proteins for Q8YBK1 (Brucella melitensis biotype 1 (strain ATCC 23456 / CCUG 17765 / NCTC 10094 / 16M)) Explore Q8YBK1 Go to UniProtKB: Q8YBK1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8YBK1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G6Q Query on G6Q Download:Ideal Coordinates CCD File SDF format, chain IC [auth B] SDF format, chain TA [auth A] MOL2 format, chain IC [auth B] MOL2 format, chain TA [auth A] mmCIF format, chain IC [auth B] mmCIF format, chain TA [auth A]	IC [auth B], TA [auth A]	GLUCOSE-6-PHOSPHATE C₆ H₁₃ O₉ P VFRROHXSMXFLSN-SLPGGIOYSA-N		Interactions Focus chain IC [auth B] Focus chain TA [auth A] Interactions & Density Focus chain IC [auth B] Focus chain TA [auth A]
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AC [auth B] SDF format, chain BA [auth A] SDF format, chain BC [auth B] SDF format, chain C [auth A] SDF format, chain CA [auth A] SDF format, chain CB [auth B] SDF format, chain D [auth A] SDF format, chain DA [auth A] SDF format, chain DB [auth B] SDF format, chain DC [auth B] SDF format, chain E [auth A] SDF format, chain EA [auth A] SDF format, chain EC [auth B] SDF format, chain F [auth A] SDF format, chain FA [auth A] SDF format, chain FB [auth B] SDF format, chain FC [auth B] SDF format, chain G [auth A] SDF format, chain GA [auth A] SDF format, chain GB [auth B] SDF format, chain H [auth A] SDF format, chain HA [auth A] SDF format, chain HB [auth B] SDF format, chain HC [auth B] SDF format, chain I [auth A] SDF format, chain IA [auth A] SDF format, chain IB [auth B] SDF format, chain JA [auth A] SDF format, chain JB [auth B] SDF format, chain K [auth A] SDF format, chain KA [auth A] SDF format, chain KB [auth B] SDF format, chain LA [auth A] SDF format, chain M [auth A] SDF format, chain MB [auth B] SDF format, chain N [auth A] SDF format, chain NA [auth A] SDF format, chain OA [auth A] SDF format, chain OB [auth B] SDF format, chain PA [auth A] SDF format, chain PB [auth B] SDF format, chain Q [auth A] SDF format, chain QA [auth A] SDF format, chain QB [auth B] SDF format, chain R [auth A] SDF format, chain RA [auth A] SDF format, chain RB [auth B] SDF format, chain S [auth A] SDF format, chain SA [auth A] SDF format, chain SB [auth B] SDF format, chain TB [auth B] SDF format, chain U [auth A] SDF format, chain UB [auth B] SDF format, chain V [auth A] SDF format, chain VB [auth B] SDF format, chain W [auth A] SDF format, chain WB [auth B] SDF format, chain X [auth A] SDF format, chain XB [auth B] SDF format, chain Y [auth A] SDF format, chain YB [auth B] SDF format, chain ZB [auth B] SDF format, chain Z [auth A] SDF format, chain T [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain NB [auth B] SDF format, chain MA [auth A] SDF format, chain LB [auth B] SDF format, chain L [auth A] SDF format, chain J [auth A] SDF format, chain GC [auth B] SDF format, chain EB [auth B] SDF format, chain CC [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain AC [auth B] MOL2 format, chain BA [auth A] MOL2 format, chain BC [auth B] MOL2 format, chain C [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth B] MOL2 format, chain D [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth B] MOL2 format, chain DC [auth B] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain EC [auth B] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain FB [auth B] MOL2 format, chain FC [auth B] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain GB [auth B] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain HB [auth B] MOL2 format, chain HC [auth B] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain IB [auth B] MOL2 format, chain JA [auth A] MOL2 format, chain JB [auth B] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain KB [auth B] MOL2 format, chain LA [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MB [auth B] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain OB [auth B] MOL2 format, chain PA [auth A] MOL2 format, chain PB [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain QB [auth B] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain RB [auth B] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth A] MOL2 format, chain SB [auth B] MOL2 format, chain TB [auth B] MOL2 format, chain U [auth A] MOL2 format, chain UB [auth B] MOL2 format, chain V [auth A] MOL2 format, chain VB [auth B] MOL2 format, chain W [auth A] MOL2 format, chain WB [auth B] MOL2 format, chain X [auth A] MOL2 format, chain XB [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain YB [auth B] MOL2 format, chain ZB [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain T [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain NB [auth B] MOL2 format, chain MA [auth A] MOL2 format, chain LB [auth B] MOL2 format, chain L [auth A] MOL2 format, chain J [auth A] MOL2 format, chain GC [auth B] MOL2 format, chain EB [auth B] MOL2 format, chain CC [auth B] mmCIF format, chain AA [auth A] mmCIF format, chain AC [auth B] mmCIF format, chain BA [auth A] mmCIF format, chain BC [auth B] mmCIF format, chain C [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain CB [auth B] mmCIF format, chain D [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain DB [auth B] mmCIF format, chain DC [auth B] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain EC [auth B] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain FB [auth B] mmCIF format, chain FC [auth B] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain GB [auth B] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain HB [auth B] mmCIF format, chain HC [auth B] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain IB [auth B] mmCIF format, chain JA [auth A] mmCIF format, chain JB [auth B] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain KB [auth B] mmCIF format, chain LA [auth A] mmCIF format, chain M [auth A] mmCIF format, chain MB [auth B] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth A] mmCIF format, chain OA [auth A] mmCIF format, chain OB [auth B] mmCIF format, chain PA [auth A] mmCIF format, chain PB [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth A] mmCIF format, chain QB [auth B] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth A] mmCIF format, chain RB [auth B] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth A] mmCIF format, chain SB [auth B] mmCIF format, chain TB [auth B] mmCIF format, chain U [auth A] mmCIF format, chain UB [auth B] mmCIF format, chain V [auth A] mmCIF format, chain VB [auth B] mmCIF format, chain W [auth A] mmCIF format, chain WB [auth B] mmCIF format, chain X [auth A] mmCIF format, chain XB [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain YB [auth B] mmCIF format, chain ZB [auth B] mmCIF format, chain Z [auth A] mmCIF format, chain T [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain NB [auth B] mmCIF format, chain MA [auth A] mmCIF format, chain LB [auth B] mmCIF format, chain L [auth A] mmCIF format, chain J [auth A] mmCIF format, chain GC [auth B] mmCIF format, chain EB [auth B] mmCIF format, chain CC [auth B]	AA [auth A] AC [auth B] BA [auth A] BC [auth B] C [auth A] AA [auth A], AC [auth B], BA [auth A], BC [auth B], C [auth A], CA [auth A], CB [auth B], CC [auth B], D [auth A], DA [auth A], DB [auth B], DC [auth B], E [auth A], EA [auth A], EB [auth B], EC [auth B], F [auth A], FA [auth A], FB [auth B], FC [auth B], G [auth A], GA [auth A], GB [auth B], GC [auth B], H [auth A], HA [auth A], HB [auth B], HC [auth B], I [auth A], IA [auth A], IB [auth B], J [auth A], JA [auth A], JB [auth B], K [auth A], KA [auth A], KB [auth B], L [auth A], LA [auth A], LB [auth B], M [auth A], MA [auth A], MB [auth B], N [auth A], NA [auth A], NB [auth B], O [auth A], OA [auth A], OB [auth B], P [auth A], PA [auth A], PB [auth B], Q [auth A], QA [auth A], QB [auth B], R [auth A], RA [auth A], RB [auth B], S [auth A], SA [auth A], SB [auth B], T [auth A], TB [auth B], U [auth A], UB [auth B], V [auth A], VB [auth B], W [auth A], WB [auth B], X [auth A], XB [auth B], Y [auth A], YB [auth B], Z [auth A], ZB [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain AA [auth A] Focus chain AC [auth B] Focus chain BA [auth A] Focus chain BC [auth B] Focus chain C [auth A] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain CC [auth B] Focus chain D [auth A] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain DC [auth B] Focus chain E [auth A] Focus chain EA [auth A] Focus chain EB [auth B] Focus chain EC [auth B] Focus chain F [auth A] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain FC [auth B] Focus chain G [auth A] Focus chain GA [auth A] Focus chain GB [auth B] Focus chain GC [auth B] Focus chain H [auth A] Focus chain HA [auth A] Focus chain HB [auth B] Focus chain HC [auth B] Focus chain I [auth A] Focus chain IA [auth A] Focus chain IB [auth B] Focus chain J [auth A] Focus chain JA [auth A] Focus chain JB [auth B] Focus chain K [auth A] Focus chain KA [auth A] Focus chain KB [auth B] Focus chain L [auth A] Focus chain LA [auth A] Focus chain LB [auth B] Focus chain M [auth A] Focus chain MA [auth A] Focus chain MB [auth B] Focus chain N [auth A] Focus chain NA [auth A] Focus chain NB [auth B] Focus chain O [auth A] Focus chain OA [auth A] Focus chain OB [auth B] Focus chain P [auth A] Focus chain PA [auth A] Focus chain PB [auth B] Focus chain Q [auth A] Focus chain QA [auth A] Focus chain QB [auth B] Focus chain R [auth A] Focus chain RA [auth A] Focus chain RB [auth B] Focus chain S [auth A] Focus chain SA [auth A] Focus chain SB [auth B] Focus chain T [auth A] Focus chain TB [auth B] Focus chain U [auth A] Focus chain UB [auth B] Focus chain V [auth A] Focus chain VB [auth B] Focus chain W [auth A] Focus chain WB [auth B] Focus chain X [auth A] Focus chain XB [auth B] Focus chain Y [auth A] Focus chain YB [auth B] Focus chain Z [auth A] Focus chain ZB [auth B] Interactions & Density Focus chain AA [auth A] Focus chain AC [auth B] Focus chain BA [auth A] Focus chain BC [auth B] Focus chain C [auth A] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain CC [auth B] Focus chain D [auth A] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain DC [auth B] Focus chain E [auth A] Focus chain EA [auth A] Focus chain EB [auth B] Focus chain EC [auth B] Focus chain F [auth A] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain FC [auth B] Focus chain G [auth A] Focus chain GA [auth A] Focus chain GB [auth B] Focus chain GC [auth B] Focus chain H [auth A] Focus chain HA [auth A] Focus chain HB [auth B] Focus chain HC [auth B] Focus chain I [auth A] Focus chain IA [auth A] Focus chain IB [auth B] Focus chain J [auth A] Focus chain JA [auth A] Focus chain JB [auth B] Focus chain K [auth A] Focus chain KA [auth A] Focus chain KB [auth B] Focus chain L [auth A] Focus chain LA [auth A] Focus chain LB [auth B] Focus chain M [auth A] Focus chain MA [auth A] Focus chain MB [auth B] Focus chain N [auth A] Focus chain NA [auth A] Focus chain NB [auth B] Focus chain O [auth A] Focus chain OA [auth A] Focus chain OB [auth B] Focus chain P [auth A] Focus chain PA [auth A] Focus chain PB [auth B] Focus chain Q [auth A] Focus chain QA [auth A] Focus chain QB [auth B] Focus chain R [auth A] Focus chain RA [auth A] Focus chain RB [auth B] Focus chain S [auth A] Focus chain SA [auth A] Focus chain SB [auth B] Focus chain T [auth A] Focus chain TB [auth B] Focus chain U [auth A] Focus chain UB [auth B] Focus chain V [auth A] Focus chain VB [auth B] Focus chain W [auth A] Focus chain WB [auth B] Focus chain X [auth A] Focus chain XB [auth B] Focus chain Y [auth A] Focus chain YB [auth B] Focus chain Z [auth A] Focus chain ZB [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain JC [auth B] SDF format, chain UA [auth A] SDF format, chain VA [auth A] SDF format, chain WA [auth A] SDF format, chain XA [auth A] SDF format, chain YA [auth A] SDF format, chain ZA [auth A] SDF format, chain AB [auth A] MOL2 format, chain JC [auth B] MOL2 format, chain UA [auth A] MOL2 format, chain VA [auth A] MOL2 format, chain WA [auth A] MOL2 format, chain XA [auth A] MOL2 format, chain YA [auth A] MOL2 format, chain ZA [auth A] MOL2 format, chain AB [auth A] mmCIF format, chain JC [auth B] mmCIF format, chain UA [auth A] mmCIF format, chain VA [auth A] mmCIF format, chain WA [auth A] mmCIF format, chain XA [auth A] mmCIF format, chain YA [auth A] mmCIF format, chain ZA [auth A] mmCIF format, chain AB [auth A]	AB [auth A] JC [auth B] UA [auth A] VA [auth A] WA [auth A] AB [auth A], JC [auth B], UA [auth A], VA [auth A], WA [auth A], XA [auth A], YA [auth A], ZA [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth A] Focus chain JC [auth B] Focus chain UA [auth A] Focus chain VA [auth A] Focus chain WA [auth A] Focus chain XA [auth A] Focus chain YA [auth A] Focus chain ZA [auth A] Interactions & Density Focus chain AB [auth A] Focus chain JC [auth B] Focus chain UA [auth A] Focus chain VA [auth A] Focus chain WA [auth A] Focus chain XA [auth A] Focus chain YA [auth A] Focus chain ZA [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain BB [auth A] SDF format, chain KC [auth B] MOL2 format, chain BB [auth A] MOL2 format, chain KC [auth B] mmCIF format, chain BB [auth A] mmCIF format, chain KC [auth B]	BB [auth A], KC [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BB [auth A] Focus chain KC [auth B] Interactions & Density Focus chain BB [auth A] Focus chain KC [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A, B	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.209 (Depositor), 0.210 (DCC)
R-Value Work: 0.174 (Depositor), 0.181 (DCC)
R-Value Observed: 0.175 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.95	α = 90
b = 55.98	β = 92.18
c = 131.67	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-11-21

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2012-11-21
Type: Initial release
Version 1.1: 2017-09-20
Changes: Data collection
Version 1.2: 2017-10-11
Changes: Data collection
Version 1.3: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary