3OCM | pdb_00003ocm

The crystal structure of a domain from a possible membrane protein of Bordetella parapertussis

PDB DOI: https://doi.org/10.2210/pdb3OCM/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Bordetella parapertussis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-08-10 Released: 2010-10-06
Deposition Author(s): Tan, K., Tesar, C., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.197 (Depositor), 0.195 (DCC)
R-Value Work:
0.173 (Depositor), 0.173 (DCC)
R-Value Observed:
0.174 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

The crystal structure of a domain from a possible membrane protein of Bordetella parapertussis

Tan, K., Tesar, C., Cobb, G., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 39.81 kDa
Atom Count: 2,740
Modeled Residue Count: 295
Deposited Residue Count: 346
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative membrane protein	A, B	173	Bordetella parapertussis	Mutation(s): 0 Gene Names: BPP2278
UniProt
Find proteins for Q7W867 (Bordetella parapertussis (strain 12822 / ATCC BAA-587 / NCTC 13253)) Explore Q7W867 Go to UniProtKB: Q7W867
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7W867
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain G [auth A] mmCIF format, chain N [auth B] mmCIF format, chain G [auth A]	G [auth A], N [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain G [auth A] Focus chain N [auth B] Interactions & Density Focus chain G [auth A] Focus chain N [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] J [auth A] O [auth B] P [auth B] H [auth A], I [auth A], J [auth A], O [auth B], P [auth B], Q [auth B], R [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] K [auth B] C [auth A], D [auth A], E [auth A], F [auth A], K [auth B], L [auth B], M [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.197 (Depositor), 0.195 (DCC)
R-Value Work: 0.173 (Depositor), 0.173 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.289	α = 90
b = 152.289	β = 90
c = 46.888	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-10-06

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2010-10-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary