3OT4 | pdb_00003ot4

Structure and Catalytic Mechanism of Bordetella bronchiseptica nicF

PDB DOI: https://doi.org/10.2210/pdb3OT4/pdb

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

Deposited: 2010-09-10 Released: 2011-09-21
Deposition Author(s): Rowlett, R.S., Snider, M.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.311 (Depositor), 0.308 (DCC)
R-Value Work:
0.241 (Depositor), 0.241 (DCC)
R-Value Observed:
0.242 (Depositor)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

Literature

Structure and catalytic mechanism of Bordetella bronchisepta nicF

Rowlett, R.S., Snider, M.J.

To be published.

Macromolecule Content

Total Structure Weight: 202.17 kDa
Atom Count: 12,175
Modeled Residue Count: 1,585
Deposited Residue Count: 1,888
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative isochorismatase	A, B, C, D, E A, B, C, D, E, F, G, H	236	Bordetella bronchiseptica	Mutation(s): 0 Gene Names: BB0275, BB1782, nicF EC: 3.5.1.107
UniProt
Find proteins for A0A0H3LKK8 (Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50)) Explore A0A0H3LKK8 Go to UniProtKB: A0A0H3LKK8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3LKK8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	A, B, C, D, E A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.311 (Depositor), 0.308 (DCC)
R-Value Work: 0.241 (Depositor), 0.241 (DCC)
R-Value Observed: 0.242 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.56	α = 90
b = 157.56	β = 90
c = 198.48	γ = 120

Software Package:

Software Name	Purpose
CrysalisPro	data collection
PHASER	phasing
REFMAC	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-09-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-09-21
Type: Initial release
Version 1.1: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2023-12-06
Changes: Data collection
Version 1.3: 2024-11-20
Changes: 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.