4KD5

substrate binding domain of putative molybdenum ABC transporter from Clostridium difficile

PDB DOI: https://doi.org/10.2210/pdb4KD5/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Clostridioides difficile 630
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-04-24 Released: 2013-05-08
Deposition Author(s): Maltseva, N., Kim, Y., Grimshaw, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.259
R-Value Work: 0.204
R-Value Observed: 0.207

wwPDB Validation 3D Report Full Report

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

Literature

Substrate binding domain of putative molybdenum ABC transporter from Clostridium difficile 630

Maltseva, N., Kim, Y., Grimshaw, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 103.48 kDa
Atom Count: 7,210
Modelled Residue Count: 913
Deposited Residue Count: 932
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC-type transport system, molybdenum-specific extracellular solute-binding protein	A [auth C], B [auth A], C [auth B], D	233	Clostridioides difficile 630	Mutation(s): 0 Gene Names: CD630_08690, modA
UniProt
Find proteins for Q18A64 (Clostridioides difficile (strain 630)) Explore Q18A64 Go to UniProtKB: Q18A64
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q18A64
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain L [auth D] MOL2 format, chain K [auth B] MOL2 format, chain L [auth D] mmCIF format, chain K [auth B] mmCIF format, chain L [auth D]	K [auth B], L [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth B] Focus chain L [auth D] Interactions & Density Focus chain K [auth B] Focus chain L [auth D]
SBT Query on SBT Download Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain I [auth C] SDF format, chain J [auth B] MOL2 format, chain G [auth C] MOL2 format, chain I [auth C] MOL2 format, chain J [auth B] mmCIF format, chain G [auth C] mmCIF format, chain I [auth C] mmCIF format, chain J [auth B]	G [auth C], I [auth C], J [auth B]	2-BUTANOL C₄ H₁₀ O BTANRVKWQNVYAZ-BYPYZUCNSA-N		Interactions Focus chain G [auth C] Focus chain I [auth C] Focus chain J [auth B] Interactions & Density Focus chain G [auth C] Focus chain I [auth C] Focus chain J [auth B]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain E [auth C] SDF format, chain F [auth C] SDF format, chain H [auth C] MOL2 format, chain E [auth C] MOL2 format, chain F [auth C] MOL2 format, chain H [auth C] mmCIF format, chain E [auth C] mmCIF format, chain F [auth C] mmCIF format, chain H [auth C]	E [auth C], F [auth C], H [auth C]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain E [auth C] Focus chain F [auth C] Focus chain H [auth C] Interactions & Density Focus chain E [auth C] Focus chain F [auth C] Focus chain H [auth C]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.259
R-Value Work: 0.204
R-Value Observed: 0.207
Space Group: C 2 2 2₁
Diffraction Data: https://doi.org/10.18430/m34kd5

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.644	α = 90
b = 141.068	β = 90
c = 122.59	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELX	model building
RESOLVE	model building
BUCCANEER	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
RESOLVE	phasing
BUCCANEER	phasing