3UHJ | pdb_00003uhj

Crystal structure of a probable glycerol dehydrogenase from Sinorhizobium meliloti 1021

PDB DOI: https://doi.org/10.2210/pdb3UHJ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Sinorhizobium meliloti
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-11-03 Released: 2011-11-23
Deposition Author(s): Agarwal, R., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., LaFleur, J., Seidel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free:
0.264 (Depositor), 0.260 (DCC)
R-Value Work:
0.197 (Depositor), 0.200 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a probable glycerol dehydrogenase from Sinorhizobium meliloti 1021

Agarwal, R., Almo, S.C., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 333.77 kDa
Atom Count: 21,320
Modeled Residue Count: 2,842
Deposited Residue Count: 3,096
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable glycerol dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H	387	Sinorhizobium meliloti	Mutation(s): 0 Gene Names: gldA, R02550, SMc02038 EC: 1.1.1.6
UniProt
Find proteins for Q92MR2 (Rhizobium meliloti (strain 1021)) Explore Q92MR2 Go to UniProtKB: Q92MR2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q92MR2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain U [auth G] SDF format, chain Q [auth E] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain U [auth G] MOL2 format, chain Q [auth E] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D] mmCIF format, chain U [auth G] mmCIF format, chain Q [auth E]	I [auth A] K [auth B] M [auth C] O [auth D] Q [auth E] I [auth A], K [auth B], M [auth C], O [auth D], Q [auth E], U [auth G]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain U [auth G] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain U [auth G]
SE Query on SE Download Ideal Coordinates CCD File SDF format, chain W [auth H] SDF format, chain R [auth E] MOL2 format, chain W [auth H] MOL2 format, chain R [auth E] mmCIF format, chain W [auth H] mmCIF format, chain R [auth E]	R [auth E], W [auth H]	SELENIUM ATOM Se SPVXKVOXSXTJOY-UHFFFAOYSA-N		Interactions Focus chain R [auth E] Focus chain W [auth H] Interactions & Density Focus chain R [auth E] Focus chain W [auth H]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain P [auth D] SDF format, chain S [auth E] SDF format, chain T [auth F] SDF format, chain V [auth G] SDF format, chain X [auth H] SDF format, chain N [auth C] SDF format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth D] MOL2 format, chain S [auth E] MOL2 format, chain T [auth F] MOL2 format, chain V [auth G] MOL2 format, chain X [auth H] MOL2 format, chain N [auth C] MOL2 format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth D] mmCIF format, chain S [auth E] mmCIF format, chain T [auth F] mmCIF format, chain V [auth G] mmCIF format, chain X [auth H] mmCIF format, chain N [auth C] mmCIF format, chain J [auth A]	J [auth A] L [auth B] N [auth C] P [auth D] S [auth E] J [auth A], L [auth B], N [auth C], P [auth D], S [auth E], T [auth F], V [auth G], X [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain X [auth H] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain X [auth H]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free: 0.264 (Depositor), 0.260 (DCC)
R-Value Work: 0.197 (Depositor), 0.200 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.483	α = 76.94
b = 98.996	β = 83.38
c = 104.734	γ = 71.47

Software Package:

Software Name	Purpose
CBASS	data collection
MOLREP	phasing
CCP4	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-11-23

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2011-11-23
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2023-12-06
Changes: Data collection
Version 1.3: 2024-10-09
Changes: Structure summary