3DKZ | pdb_00003dkz

Crystal structure of the Q7W9W5_BORPA protein from Bordetella parapertussis. Northeast Structural Genomics Consortium target BpR208C.

PDB DOI: https://doi.org/10.2210/pdb3DKZ/pdb

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

Deposited: 2008-06-26 Released: 2008-08-26
Deposition Author(s): Vorobiev, S.M., Su, M., Seetharaman, J., Wang, D., Ciccosanti, C., Foote, E.L., Mao, L., Xiao, R., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.260 (Depositor), 0.281 (DCC)
R-Value Work:
0.238 (Depositor), 0.253 (DCC)
R-Value Observed:
0.238 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the Q7W9W5_BORPA protein from Bordetella parapertussis.

Vorobiev, S.M., Su, M., Seetharaman, J., Wang, D., Ciccosanti, C., Foote, E.L., Mao, L., Xiao, R., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 31.16 kDa
Atom Count: 1,894
Modeled Residue Count: 249
Deposited Residue Count: 284
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioesterase superfamily protein	A, B	142	Bordetella parapertussis	Mutation(s): 0 Gene Names: BPP1634
UniProt
Find proteins for Q7W9W5 (Bordetella parapertussis (strain 12822 / ATCC BAA-587 / NCTC 13253)) Explore Q7W9W5 Go to UniProtKB: Q7W9W5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7W9W5
Sequence Annotations Expand
Reference Sequence

Small Molecules

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: 2.40 Å
R-Value Free: 0.260 (Depositor), 0.281 (DCC)
R-Value Work: 0.238 (Depositor), 0.253 (DCC)
R-Value Observed: 0.238 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.646	α = 90
b = 69.646	β = 90
c = 107.792	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
SHELXDE	phasing
RESOLVE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-08-26

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2008-08-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Structure summary