3C5Y | pdb_00003c5y

Crystal structure of a putative ribose 5-phosphate isomerase (saro_3514) from novosphingobium aromaticivorans dsm at 1.81 A resolution

PDB DOI: https://doi.org/10.2210/pdb3C5Y/pdb

Classification: ISOMERASE
Organism(s): Novosphingobium aromaticivorans DSM 12444
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-02-01 Released: 2008-02-19
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free:
0.220 (Depositor), 0.225 (DCC)
R-Value Work:
0.170 (Depositor), 0.178 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.8 of the entry. See complete history.

Literature

Crystal structure of putative ribose 5-phosphate isomerase (YP_001165900.1) from Novosphingobium aromaticivorans DSM 12444 at 1.81 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 417.47 kDa
Atom Count: 28,863
Modeled Residue Count: 3,394
Deposited Residue Count: 3,696
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribose/galactose isomerase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	231	Novosphingobium aromaticivorans DSM 12444	Mutation(s): 0 Gene Names: YP_001165900.1, Saro_3514
UniProt
Find proteins for A4XEL3 (Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199)) Explore A4XEL3 Go to UniProtKB: A4XEL3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A4XEL3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth G] SDF format, chain AC [auth M] SDF format, chain BA [auth B] SDF format, chain BB [auth G] SDF format, chain BC [auth M] SDF format, chain CA [auth B] SDF format, chain CB [auth G] SDF format, chain CC [auth N] SDF format, chain DA [auth B] SDF format, chain DB [auth G] SDF format, chain DC [auth N] SDF format, chain EA [auth C] SDF format, chain EB [auth G] SDF format, chain EC [auth N] SDF format, chain FA [auth C] SDF format, chain FB [auth G] SDF format, chain GA [auth D] SDF format, chain GB [auth H] SDF format, chain GC [auth P] SDF format, chain HA [auth D] SDF format, chain HB [auth H] SDF format, chain IA [auth E] SDF format, chain IB [auth H] SDF format, chain JA [auth E] SDF format, chain JB [auth H] SDF format, chain KA [auth E] SDF format, chain KB [auth H] SDF format, chain LA [auth E] SDF format, chain LB [auth H] SDF format, chain MA [auth E] SDF format, chain NB [auth I] SDF format, chain OB [auth I] SDF format, chain PB [auth I] SDF format, chain Q [auth A] SDF format, chain QB [auth I] SDF format, chain R [auth A] SDF format, chain RA [auth F] SDF format, chain RB [auth J] SDF format, chain S [auth A] SDF format, chain SA [auth F] SDF format, chain SB [auth J] SDF format, chain T [auth A] SDF format, chain TA [auth F] SDF format, chain TB [auth J] SDF format, chain U [auth A] SDF format, chain UA [auth F] SDF format, chain UB [auth K] SDF format, chain V [auth A] SDF format, chain VA [auth F] SDF format, chain VB [auth K] SDF format, chain W [auth A] SDF format, chain WA [auth F] SDF format, chain WB [auth K] SDF format, chain X [auth A] SDF format, chain XB [auth L] SDF format, chain Y [auth B] SDF format, chain YB [auth M] SDF format, chain Z [auth B] SDF format, chain ZA [auth G] SDF format, chain ZB [auth M] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth G] MOL2 format, chain AC [auth M] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth G] MOL2 format, chain BC [auth M] MOL2 format, chain CA [auth B] MOL2 format, chain CB [auth G] MOL2 format, chain CC [auth N] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth G] MOL2 format, chain DC [auth N] MOL2 format, chain EA [auth C] MOL2 format, chain EB [auth G] MOL2 format, chain EC [auth N] MOL2 format, chain FA [auth C] MOL2 format, chain FB [auth G] MOL2 format, chain GA [auth D] MOL2 format, chain GB [auth H] MOL2 format, chain GC [auth P] MOL2 format, chain HA [auth D] MOL2 format, chain HB [auth H] MOL2 format, chain IA [auth E] MOL2 format, chain IB [auth H] MOL2 format, chain JA [auth E] MOL2 format, chain JB [auth H] MOL2 format, chain KA [auth E] MOL2 format, chain KB [auth H] MOL2 format, chain LA [auth E] MOL2 format, chain LB [auth H] MOL2 format, chain MA [auth E] MOL2 format, chain NB [auth I] MOL2 format, chain OB [auth I] MOL2 format, chain PB [auth I] MOL2 format, chain Q [auth A] MOL2 format, chain QB [auth I] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth F] MOL2 format, chain RB [auth J] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth F] MOL2 format, chain SB [auth J] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth F] MOL2 format, chain TB [auth J] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth F] MOL2 format, chain UB [auth K] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth F] MOL2 format, chain VB [auth K] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth F] MOL2 format, chain WB [auth K] MOL2 format, chain X [auth A] MOL2 format, chain XB [auth L] MOL2 format, chain Y [auth B] MOL2 format, chain YB [auth M] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth G] MOL2 format, chain ZB [auth M] mmCIF format, chain AA [auth B] mmCIF format, chain AB [auth G] mmCIF format, chain AC [auth M] mmCIF format, chain BA [auth B] mmCIF format, chain BB [auth G] mmCIF format, chain BC [auth M] mmCIF format, chain CA [auth B] mmCIF format, chain CB [auth G] mmCIF format, chain CC [auth N] mmCIF format, chain DA [auth B] mmCIF format, chain DB [auth G] mmCIF format, chain DC [auth N] mmCIF format, chain EA [auth C] mmCIF format, chain EB [auth G] mmCIF format, chain EC [auth N] mmCIF format, chain FA [auth C] mmCIF format, chain FB [auth G] mmCIF format, chain GA [auth D] mmCIF format, chain GB [auth H] mmCIF format, chain GC [auth P] mmCIF format, chain HA [auth D] mmCIF format, chain HB [auth H] mmCIF format, chain IA [auth E] mmCIF format, chain IB [auth H] mmCIF format, chain JA [auth E] mmCIF format, chain JB [auth H] mmCIF format, chain KA [auth E] mmCIF format, chain KB [auth H] mmCIF format, chain LA [auth E] mmCIF format, chain LB [auth H] mmCIF format, chain MA [auth E] mmCIF format, chain NB [auth I] mmCIF format, chain OB [auth I] mmCIF format, chain PB [auth I] mmCIF format, chain Q [auth A] mmCIF format, chain QB [auth I] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth F] mmCIF format, chain RB [auth J] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth F] mmCIF format, chain SB [auth J] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth F] mmCIF format, chain TB [auth J] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth F] mmCIF format, chain UB [auth K] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth F] mmCIF format, chain VB [auth K] mmCIF format, chain W [auth A] mmCIF format, chain WA [auth F] mmCIF format, chain WB [auth K] mmCIF format, chain X [auth A] mmCIF format, chain XB [auth L] mmCIF format, chain Y [auth B] mmCIF format, chain YB [auth M] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth G] mmCIF format, chain ZB [auth M]	AA [auth B] AB [auth G] AC [auth M] BA [auth B] BB [auth G] AA [auth B], AB [auth G], AC [auth M], BA [auth B], BB [auth G], BC [auth M], CA [auth B], CB [auth G], CC [auth N], DA [auth B], DB [auth G], DC [auth N], EA [auth C], EB [auth G], EC [auth N], FA [auth C], FB [auth G], GA [auth D], GB [auth H], GC [auth P], HA [auth D], HB [auth H], IA [auth E], IB [auth H], JA [auth E], JB [auth H], KA [auth E], KB [auth H], LA [auth E], LB [auth H], MA [auth E], NB [auth I], OB [auth I], PB [auth I], Q [auth A], QB [auth I], R [auth A], RA [auth F], RB [auth J], S [auth A], SA [auth F], SB [auth J], T [auth A], TA [auth F], TB [auth J], U [auth A], UA [auth F], UB [auth K], V [auth A], VA [auth F], VB [auth K], W [auth A], WA [auth F], WB [auth K], X [auth A], XB [auth L], Y [auth B], YB [auth M], Z [auth B], ZA [auth G], ZB [auth M]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth G] Focus chain AC [auth M] Focus chain BA [auth B] Focus chain BB [auth G] Focus chain BC [auth M] Focus chain CA [auth B] Focus chain CB [auth G] Focus chain CC [auth N] Focus chain DA [auth B] Focus chain DB [auth G] Focus chain DC [auth N] Focus chain EA [auth C] Focus chain EB [auth G] Focus chain EC [auth N] Focus chain FA [auth C] Focus chain FB [auth G] Focus chain GA [auth D] Focus chain GB [auth H] Focus chain GC [auth P] Focus chain HA [auth D] Focus chain HB [auth H] Focus chain IA [auth E] Focus chain IB [auth H] Focus chain JA [auth E] Focus chain JB [auth H] Focus chain KA [auth E] Focus chain KB [auth H] Focus chain LA [auth E] Focus chain LB [auth H] Focus chain MA [auth E] Focus chain NB [auth I] Focus chain OB [auth I] Focus chain PB [auth I] Focus chain Q [auth A] Focus chain QB [auth I] Focus chain R [auth A] Focus chain RA [auth F] Focus chain RB [auth J] Focus chain S [auth A] Focus chain SA [auth F] Focus chain SB [auth J] Focus chain T [auth A] Focus chain TA [auth F] Focus chain TB [auth J] Focus chain U [auth A] Focus chain UA [auth F] Focus chain UB [auth K] Focus chain V [auth A] Focus chain VA [auth F] Focus chain VB [auth K] Focus chain W [auth A] Focus chain WA [auth F] Focus chain WB [auth K] Focus chain X [auth A] Focus chain XB [auth L] Focus chain Y [auth B] Focus chain YB [auth M] Focus chain Z [auth B] Focus chain ZA [auth G] Focus chain ZB [auth M] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth G] Focus chain AC [auth M] Focus chain BA [auth B] Focus chain BB [auth G] Focus chain BC [auth M] Focus chain CA [auth B] Focus chain CB [auth G] Focus chain CC [auth N] Focus chain DA [auth B] Focus chain DB [auth G] Focus chain DC [auth N] Focus chain EA [auth C] Focus chain EB [auth G] Focus chain EC [auth N] Focus chain FA [auth C] Focus chain FB [auth G] Focus chain GA [auth D] Focus chain GB [auth H] Focus chain GC [auth P] Focus chain HA [auth D] Focus chain HB [auth H] Focus chain IA [auth E] Focus chain IB [auth H] Focus chain JA [auth E] Focus chain JB [auth H] Focus chain KA [auth E] Focus chain KB [auth H] Focus chain LA [auth E] Focus chain LB [auth H] Focus chain MA [auth E] Focus chain NB [auth I] Focus chain OB [auth I] Focus chain PB [auth I] Focus chain Q [auth A] Focus chain QB [auth I] Focus chain R [auth A] Focus chain RA [auth F] Focus chain RB [auth J] Focus chain S [auth A] Focus chain SA [auth F] Focus chain SB [auth J] Focus chain T [auth A] Focus chain TA [auth F] Focus chain TB [auth J] Focus chain U [auth A] Focus chain UA [auth F] Focus chain UB [auth K] Focus chain V [auth A] Focus chain VA [auth F] Focus chain VB [auth K] Focus chain W [auth A] Focus chain WA [auth F] Focus chain WB [auth K] Focus chain X [auth A] Focus chain XB [auth L] Focus chain Y [auth B] Focus chain YB [auth M] Focus chain Z [auth B] Focus chain ZA [auth G] Focus chain ZB [auth M]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain FC [auth P] SDF format, chain MB [auth I] SDF format, chain NA [auth F] SDF format, chain OA [auth F] SDF format, chain PA [auth F] SDF format, chain QA [auth F] SDF format, chain XA [auth G] SDF format, chain YA [auth G] MOL2 format, chain FC [auth P] MOL2 format, chain MB [auth I] MOL2 format, chain NA [auth F] MOL2 format, chain OA [auth F] MOL2 format, chain PA [auth F] MOL2 format, chain QA [auth F] MOL2 format, chain XA [auth G] MOL2 format, chain YA [auth G] mmCIF format, chain FC [auth P] mmCIF format, chain MB [auth I] mmCIF format, chain NA [auth F] mmCIF format, chain OA [auth F] mmCIF format, chain PA [auth F] mmCIF format, chain QA [auth F] mmCIF format, chain XA [auth G] mmCIF format, chain YA [auth G]	FC [auth P] MB [auth I] NA [auth F] OA [auth F] PA [auth F] FC [auth P], MB [auth I], NA [auth F], OA [auth F], PA [auth F], QA [auth F], XA [auth G], YA [auth G]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain FC [auth P] Focus chain MB [auth I] Focus chain NA [auth F] Focus chain OA [auth F] Focus chain PA [auth F] Focus chain QA [auth F] Focus chain XA [auth G] Focus chain YA [auth G] Interactions & Density Focus chain FC [auth P] Focus chain MB [auth I] Focus chain NA [auth F] Focus chain OA [auth F] Focus chain PA [auth F] Focus chain QA [auth F] Focus chain XA [auth G] Focus chain YA [auth G]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD Query on CSD	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	L-PEPTIDE LINKING	C₃ H₇ N O₄ S		CYS
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free: 0.220 (Depositor), 0.225 (DCC)
R-Value Work: 0.170 (Depositor), 0.178 (DCC)
R-Value Observed: 0.173 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.754	α = 90
b = 109.462	β = 102.92
c = 167.569	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
MOLREP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-02-19

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2008-02-19
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2014-11-12
Changes: Structure summary
Version 1.3: 2017-10-25
Changes: Refinement description
Version 1.4: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.5: 2023-02-01
Changes: Database references, Derived calculations
Version 1.6: 2023-09-20
Changes: Data collection, Refinement description
Version 1.7: 2023-11-15
Changes: Data collection
Version 1.8: 2024-11-20
Changes: Structure summary