4MLC | pdb_00004mlc

ABC Transporter Substrate-Binding Protein fromDesulfitobacterium hafniense

PDB DOI: https://doi.org/10.2210/pdb4MLC/pdb

Classification: SIGNALING PROTEIN
Organism(s): Desulfitobacterium hafniense DCB-2
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2013-09-06 Released: 2013-09-18
Deposition Author(s): Kim, Y., Chhor, G., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.71 Å
R-Value Free:
0.219 (Depositor), 0.227 (DCC)
R-Value Work:
0.166 (Depositor), 0.171 (DCC)
R-Value Observed:
0.171 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4MLC

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

Literature

ABC Transporter Substrate-Binding Protein fromDesulfitobacterium hafniense

Kim, Y., Chhor, G., Endres, M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 39.49 kDa
Atom Count: 2,665
Modeled Residue Count: 336
Deposited Residue Count: 356
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Extracellular ligand-binding receptor	A	356	Desulfitobacterium hafniense DCB-2	Mutation(s): 0 Gene Names: Dhaf_0110
UniProt
Find proteins for B8FZ96 (Desulfitobacterium hafniense (strain DSM 10664 / DCB-2)) Explore B8FZ96 Go to UniProtKB: B8FZ96
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B8FZ96
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.71 Å
R-Value Free: 0.219 (Depositor), 0.227 (DCC)
R-Value Work: 0.166 (Depositor), 0.171 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.195	α = 90
b = 81.796	β = 90
c = 128.739	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-09-18

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2013-09-18
Type: Initial release
Version 1.1: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.