4HKT

Crystal structure of a putative myo-inositol dehydrogenase from Sinorhizobium meliloti 1021 (Target PSI-012312)

PDB DOI: https://doi.org/10.2210/pdb4HKT/pdb

Classification: OXIDOREDUCTASE
Organism(s): Sinorhizobium meliloti 1021
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-10-15 Released: 2012-12-19
Deposition Author(s): Sampathkumar, P., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.232
R-Value Work: 0.186
R-Value Observed: 0.188

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a putative myo-inositoldehydrogenase from Sinorhizobium meliloti 1021 (Target PSI-012312)

Sampathkumar, P., Gizzi, A., Ahmed, M., Banu, N., Bhosle, R., Bonanno, J., Chamala, S., Chowdhury, S., Fiser, A., Glenn, A.S., Hammonds, J., Hillerich, B., Khafizov, K., Lafleur, J., Love, J.D., Stead, M., Seidel, R., Toro, R., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 144.3 kDa
Atom Count: 10,688
Modelled Residue Count: 1,317
Deposited Residue Count: 1,324
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inositol 2-dehydrogenase	A, B, C, D	331	Sinorhizobium meliloti 1021	Mutation(s): 0 Gene Names: idhA, iolG, RB1194, SMb20899, SM_b20899 EC: 1.1.1.18
UniProt
Find proteins for O68965 (Rhizobium meliloti (strain 1021)) Explore O68965 Go to UniProtKB: O68965
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O68965
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 BA [auth B] SDF format, chain EA [auth C] SDF format, chain GA [auth D] SDF format, chain P [auth A] SDF format, chain Q [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A]	BA [auth B], EA [auth C], GA [auth D], P [auth A], Q [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain EA [auth C] Focus chain GA [auth D] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain BA [auth B] Focus chain EA [auth C] Focus chain GA [auth D] Focus chain P [auth A] Focus chain Q [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain H [auth A] SDF format, chain N [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain Y [auth B] SDF format, chain CA [auth C] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain FA [auth D] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain T [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Z [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain N [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain T [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Z [auth B]	CA [auth C] DA [auth C] E [auth A] F [auth A] FA [auth D] CA [auth C], DA [auth C], E [auth A], F [auth A], FA [auth D], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain AA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain AA [auth B]	AA [auth B], O [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain O [auth A] Interactions & Density Focus chain AA [auth B] Focus chain O [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.232
R-Value Work: 0.186
R-Value Observed: 0.188
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.449	α = 90
b = 55.467	β = 97.56
c = 149.091	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-3000	data reduction
SCALEPACK	data scaling
SHELX	phasing
SHELXD	phasing
SHELXE	model building