4NHE | pdb_00004nhe

The crystal structure of oxidoreductase (Gfo/Idh/MocA family) from Streptococcus pneumoniae TIGR4 in complex with NADP

PDB DOI: https://doi.org/10.2210/pdb4NHE/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptococcus pneumoniae TIGR4
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-11-04 Released: 2013-11-27
Deposition Author(s): Tan, K., Hatzos-Skintges, C., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.207 (Depositor), 0.210 (DCC)
R-Value Work:
0.176 (Depositor), 0.180 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The crystal structure of oxidoreductase (Gfo/Idh/MocA family) from Streptococcus pneumoniae TIGR4 in complex with NADP.

Tan, K., Hatzos-Skintges, C., Jedrzejczak, R., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 113.21 kDa
Atom Count: 8,491
Modeled Residue Count: 977
Deposited Residue Count: 984
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase, Gfo/Idh/MocA family	A, B, C	328	Streptococcus pneumoniae TIGR4	Mutation(s): 0 Gene Names: SP_1482
UniProt
Find proteins for A0A0H2UR04 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2UR04 Go to UniProtKB: A0A0H2UR04
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H2UR04
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain H [auth B] SDF format, chain D [auth A] MOL2 format, chain N [auth C] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] mmCIF format, chain N [auth C] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A]	D [auth A], H [auth B], N [auth C]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Focus chain N [auth C] Interactions & Density Focus chain D [auth A] Focus chain H [auth B] Focus chain N [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain M [auth B] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain M [auth B] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain M [auth B]	M [auth B], U [auth C], V [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain M [auth B] Focus chain U [auth C] Focus chain V [auth C]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain W [auth C] MOL2 format, chain W [auth C] mmCIF format, chain W [auth C]	W [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain W [auth C] Interactions & Density Focus chain W [auth C]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] I [auth B] J [auth B] E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], L [auth B], O [auth C], P [auth C], Q [auth C], R [auth C], S [auth C], T [auth C]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.207 (Depositor), 0.210 (DCC)
R-Value Work: 0.176 (Depositor), 0.180 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.768	α = 90
b = 195.905	β = 90
c = 349.301	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
MOLREP	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-11-27

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2013-11-27
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description