3UUW

1.63 Angstrom Resolution Crystal Structure of Dehydrogenase (MviM) from Clostridium difficile.

PDB DOI: https://doi.org/10.2210/pdb3UUW/pdb

Classification: OXIDOREDUCTASE
Organism(s): Clostridioides difficile 630
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-11-28 Released: 2011-12-21
Deposition Author(s): Minasov, G., Wawrzak, Z., Kudritska, M., Grimshaw, S., Papazisi, L., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free: 0.195
R-Value Work: 0.158
R-Value Observed: 0.160

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

1.63 Angstrom Resolution Crystal Structure of Dehydrogenase (MviM) from Clostridium difficile.

Minasov, G., Wawrzak, Z., Kudritska, M., Grimshaw, S., Papazisi, L., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 141.41 kDa
Atom Count: 11,499
Modelled Residue Count: 1,213
Deposited Residue Count: 1,232
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative oxidoreductase with NAD(P)-binding Rossmann-fold domain	A, B, C, D	308	Clostridioides difficile 630	Mutation(s): 0 Gene Names: CD630_34500, mviM
UniProt
Find proteins for Q180U8 (Clostridioides difficile (strain 630)) Explore Q180U8 Go to UniProtKB: Q180U8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q180U8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A]	K [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain U [auth C] MOL2 format, chain U [auth C]	U [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain U [auth C] Interactions & Density Focus chain U [auth C]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain J [auth A] SDF format, chain P [auth B] SDF format, chain V [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain P [auth B] MOL2 format, chain V [auth C]	AA [auth D], J [auth A], P [auth B], V [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain J [auth A] Focus chain P [auth B] Focus chain V [auth C] Interactions & Density Focus chain AA [auth D] Focus chain J [auth A] Focus chain P [auth B] Focus chain V [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain T [auth C] SDF format, chain Z [auth D] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain T [auth C] MOL2 format, chain Z [auth D]	I [auth A], O [auth B], T [auth C], Z [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain O [auth B] Focus chain T [auth C] Focus chain Z [auth D] Interactions & Density Focus chain I [auth A] Focus chain O [auth B] Focus chain T [auth C] Focus chain Z [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D]	E [auth A] F [auth A] G [auth A] H [auth A] L [auth B] E [auth A], F [auth A], G [auth A], H [auth A], L [auth B], M [auth B], N [auth B], Q [auth C], R [auth C], S [auth C], W [auth D], X [auth D], Y [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free: 0.195
R-Value Work: 0.158
R-Value Observed: 0.160
Space Group: P 1
Diffraction Data: https://doi.org/10.18430/M33UUW

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.521	α = 98.1
b = 69.535	β = 106.97
c = 83.098	γ = 115.73

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-12-21

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2011-12-21
Type: Initial release
Version 1.1: 2012-01-18
Changes: Other
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2018-01-24
Changes: Structure summary
Version 1.4: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description