4KD5 | pdb_00004kd5

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 (Depositor), 0.259 (DCC)
R-Value Work:
0.204 (Depositor), 0.204 (DCC)
R-Value Observed:
0.207 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

A high-throughput structural system biology approach to increase structure representation of proteins from Clostridioides difficile.

Rosas-Lemus, M., Dey, S., Minasov, G., Tan, K., Anderson, S.M., Brunzelle, J., Nocadello, S., Shabalin, I., Filippova, E., Halavaty, A., Kim, Y., Maltseva, N., Osipiuk, J., Minor, W., Joachimiak, A., Savchenko, A., Anderson, W.F., Satchell, K.J.F.

(2023) Microbiol Resour Announc 12: e0050723-e0050723

PubMed: 37747257 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1128/MRA.00507-23
Primary Citation of Related Structures:
3SRT, 4GIB, 4H3D, 4ISX, 4KD5, 4MFG, 4NMY, 4RN7, 5DZS, 5TTA, 5TV7, 6N7M, 7K1U, 7RL8, 7RLR

PubMed Abstract:
Clostridioides difficile causes life-threatening gastrointestinal infections. It is a high-risk pathogen due to a lack of effective treatments, antimicrobial resistance, and a poorly conserved genomic core. Herein, we report 30 X-ray structures from a structure genomics pipeline spanning 13 years, representing 10.2% of the X-ray structures for this important pathogen.

Organizational Affiliation

Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.

Macromolecule Content

Total Structure Weight: 103.48 kDa
Atom Count: 7,210
Modeled 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 L [auth D] SDF format, chain K [auth B] MOL2 format, chain L [auth D] MOL2 format, chain K [auth B] mmCIF format, chain L [auth D] mmCIF format, chain K [auth B]	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 J [auth B] SDF format, chain I [auth C] SDF format, chain G [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth C] MOL2 format, chain G [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth C] mmCIF format, chain G [auth C]	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 H [auth C] SDF format, chain F [auth C] SDF format, chain E [auth C] MOL2 format, chain H [auth C] MOL2 format, chain F [auth C] MOL2 format, chain E [auth C] mmCIF format, chain H [auth C] mmCIF format, chain F [auth C] mmCIF format, chain E [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 (Depositor), 0.259 (DCC)
R-Value Work: 0.204 (Depositor), 0.204 (DCC)
R-Value Observed: 0.207 (Depositor)

Diffraction Data: https://doi.org/10.18430/m34kd5

Space Group: C 2 2 2₁

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-05-08

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2013-05-08
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.3: 2026-03-25
Changes: Database references