3BJQ | pdb_00003bjq

CRYSTAL STRUCTURE OF A PHAGE-RELATED PROTEIN (BB3626) FROM BORDETELLA BRONCHISEPTICA RB50 AT 2.05 A RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb3BJQ/pdb

Classification: VIRAL PROTEIN
Organism(s): Bordetella bronchiseptica RB50
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-12-04 Released: 2007-12-18
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.227 (Depositor), 0.280 (DCC)
R-Value Work:
0.186 (Depositor), 0.190 (DCC)
R-Value Observed:
0.186 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of phage-related protein (NP_890161.1) from Bordetella bronchiseptica at 2.05 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 353.72 kDa
Atom Count: 24,467
Modeled Residue Count: 2,975
Deposited Residue Count: 3,160
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phage-related protein	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	316	Bordetella bronchiseptica RB50	Mutation(s): 0 Gene Names: NP_890161.1, BB3626
UniProt
Find proteins for A0A0H3LS71 (Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50)) Explore A0A0H3LS71 Go to UniProtKB: A0A0H3LS71
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H3LS71
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain BA [auth H] SDF format, chain CA [auth H] SDF format, chain DA [auth I] SDF format, chain EA [auth I] SDF format, chain FA [auth J] SDF format, chain GA [auth J] SDF format, chain K [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain U [auth E] SDF format, chain V [auth E] SDF format, chain W [auth F] SDF format, chain X [auth F] SDF format, chain Y [auth G] SDF format, chain Z [auth G] MOL2 format, chain AA [auth G] MOL2 format, chain BA [auth H] MOL2 format, chain CA [auth H] MOL2 format, chain DA [auth I] MOL2 format, chain EA [auth I] MOL2 format, chain FA [auth J] MOL2 format, chain GA [auth J] MOL2 format, chain K [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain U [auth E] MOL2 format, chain V [auth E] MOL2 format, chain W [auth F] MOL2 format, chain X [auth F] MOL2 format, chain Y [auth G] MOL2 format, chain Z [auth G] mmCIF format, chain AA [auth G] mmCIF format, chain BA [auth H] mmCIF format, chain CA [auth H] mmCIF format, chain DA [auth I] mmCIF format, chain EA [auth I] mmCIF format, chain FA [auth J] mmCIF format, chain GA [auth J] mmCIF format, chain K [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D] mmCIF format, chain U [auth E] mmCIF format, chain V [auth E] mmCIF format, chain W [auth F] mmCIF format, chain X [auth F] mmCIF format, chain Y [auth G] mmCIF format, chain Z [auth G]	AA [auth G] BA [auth H] CA [auth H] DA [auth I] EA [auth I] AA [auth G], BA [auth H], CA [auth H], DA [auth I], EA [auth I], FA [auth J], GA [auth J], K [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth C], Q [auth C], S [auth D], T [auth D], U [auth E], V [auth E], W [auth F], X [auth F], Y [auth G], Z [auth G]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain BA [auth H] Focus chain CA [auth H] Focus chain DA [auth I] Focus chain EA [auth I] Focus chain FA [auth J] Focus chain GA [auth J] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth F] Focus chain X [auth F] Focus chain Y [auth G] Focus chain Z [auth G] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth H] Focus chain CA [auth H] Focus chain DA [auth I] Focus chain EA [auth I] Focus chain FA [auth J] Focus chain GA [auth J] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth F] Focus chain X [auth F] Focus chain Y [auth G] Focus chain Z [auth G]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain R [auth D] MOL2 format, chain R [auth D] mmCIF format, chain R [auth D]	R [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain R [auth D] Interactions & Density Focus chain R [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.227 (Depositor), 0.280 (DCC)
R-Value Work: 0.186 (Depositor), 0.190 (DCC)
R-Value Observed: 0.186 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33BJQ

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.39	α = 90
b = 188.32	β = 106.6
c = 105.15	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing
SHELXD	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-12-18

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2007-12-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2011-09-07
Changes: Other
Version 1.3: 2017-10-25
Changes: Refinement description
Version 1.4: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.5: 2023-01-25
Changes: Database references, Derived calculations
Version 1.6: 2024-10-30
Changes: Data collection, Refinement description, Structure summary