4MGG | pdb_00004mgg

Crystal structure of an enolase (mandelate racemase subgroup) from labrenzia aggregata iam 12614 (target nysgrc-012903) with bound mg, space group p212121

PDB DOI: https://doi.org/10.2210/pdb4MGG/pdb

Classification: ISOMERASE
Organism(s): Roseibium aggregatum IAM 12614
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-08-28 Released: 2013-10-16
Deposition Author(s): Vetting, M.W., Zhang, X., Wasserman, S.R., Morisco, L.L., Sojitra, S., Bonanno, J.B., Gerlt, J.A., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.216 (Depositor), 0.215 (DCC)
R-Value Work:
0.150 (Depositor), 0.155 (DCC)
R-Value Observed:
0.154 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of an enolase (mandelate racemase subgroup) from labrenzia aggregata iam 12614 (target nysgrc-012903) with bound mg, space group p212121

Vetting, M.W., Zhang, X., Wasserman, S.R., Morisco, L.L., Sojitra, S., Bonanno, J.B., Gerlt, J.A., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

To be published.

Macromolecule Content

Total Structure Weight: 319.91 kDa
Atom Count: 23,886
Modeled Residue Count: 2,894
Deposited Residue Count: 2,952
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Muconate lactonizing enzyme	A, B, C, D, E A, B, C, D, E, F, G, H	369	Roseibium aggregatum IAM 12614	Mutation(s): 0 Gene Names: SIAM614_28497 EC: 4.2.1.171
UniProt
Find proteins for A0NXQ8 (Roseibium aggregatum (strain ATCC 25650 / DSM 13394 / JCM 20685 / NBRC 16684 / NCIMB 2208 / IAM 12614 / B1)) Explore A0NXQ8 Go to UniProtKB: A0NXQ8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0NXQ8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain P [auth C] SDF format, chain J [auth A] MOL2 format, chain S [auth D] MOL2 format, chain P [auth C] MOL2 format, chain J [auth A] mmCIF format, chain S [auth D] mmCIF format, chain P [auth C] mmCIF format, chain J [auth A]	J [auth A], P [auth C], S [auth D]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain P [auth C] Focus chain S [auth D] Interactions & Density Focus chain J [auth A] Focus chain P [auth C] Focus chain S [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain I [auth A] SDF format, chain CA [auth G] MOL2 format, chain O [auth B] MOL2 format, chain I [auth A] MOL2 format, chain CA [auth G] mmCIF format, chain O [auth B] mmCIF format, chain I [auth A] mmCIF format, chain CA [auth G]	CA [auth G], I [auth A], O [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth G] Focus chain I [auth A] Focus chain O [auth B] Interactions & Density Focus chain CA [auth G] Focus chain I [auth A] Focus chain O [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Z [auth G] SDF format, chain Y [auth F] SDF format, chain X [auth F] SDF format, chain W [auth E] SDF format, chain V [auth E] SDF format, chain U [auth D] SDF format, chain T [auth D] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain EA [auth H] SDF format, chain DA [auth H] SDF format, chain BA [auth G] SDF format, chain AA [auth G] MOL2 format, chain Z [auth G] MOL2 format, chain Y [auth F] MOL2 format, chain X [auth F] MOL2 format, chain W [auth E] MOL2 format, chain V [auth E] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain EA [auth H] MOL2 format, chain DA [auth H] MOL2 format, chain BA [auth G] MOL2 format, chain AA [auth G] mmCIF format, chain Z [auth G] mmCIF format, chain Y [auth F] mmCIF format, chain X [auth F] mmCIF format, chain W [auth E] mmCIF format, chain V [auth E] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain EA [auth H] mmCIF format, chain DA [auth H] mmCIF format, chain BA [auth G] mmCIF format, chain AA [auth G]	AA [auth G] BA [auth G] DA [auth H] EA [auth H] K [auth A] AA [auth G], BA [auth G], DA [auth H], EA [auth H], K [auth A], L [auth A], M [auth B], N [auth B], Q [auth C], R [auth C], T [auth D], U [auth D], V [auth E], W [auth E], X [auth F], Y [auth F], Z [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain BA [auth G] Focus chain DA [auth H] Focus chain EA [auth H] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth E] Focus chain W [auth E] Focus chain X [auth F] Focus chain Y [auth F] Focus chain Z [auth G] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth G] Focus chain DA [auth H] Focus chain EA [auth H] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth E] Focus chain W [auth E] Focus chain X [auth F] Focus chain Y [auth F] Focus chain Z [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.216 (Depositor), 0.215 (DCC)
R-Value Work: 0.150 (Depositor), 0.155 (DCC)
R-Value Observed: 0.154 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.313	α = 90
b = 154.897	β = 90
c = 181.983	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
AMoRE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-10-16

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2013-10-16
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description