2H98 | pdb_00002h98

Crystal structure of the effector binding domain of a CatM variant, CatM(V158M)

PDB DOI: https://doi.org/10.2210/pdb2H98/pdb

Classification: TRANSCRIPTION
Organism(s): Acinetobacter baylyi ADP1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2006-06-09 Released: 2007-06-26
Deposition Author(s): Ezezika, O.C., Neidle, E.L., Momany, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.232 (Depositor), 0.268 (DCC)
R-Value Work:
0.167 (Depositor), 0.218 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2H98

This is version 1.5 of the entry. See complete history.

Literature

Structural basis for the altered regulatory roles of three LysR-type transcritional variants of CatM and BenM: CatM(V158M), CatM(R156H) and BenM(R156H/T157S)

Ezezika, O.C., Neidle, E.L., Momany, C.

To be published.

Macromolecule Content

Total Structure Weight: 70.93 kDa
Atom Count: 4,146
Modeled Residue Count: 432
Deposited Residue Count: 626
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional regulator catM	A, B	313	Acinetobacter baylyi ADP1	Mutation(s): 1 Gene Names: catM, catR
UniProt
Find proteins for P07774 (Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)) Explore P07774 Go to UniProtKB: P07774
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07774
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.232 (Depositor), 0.268 (DCC)
R-Value Work: 0.167 (Depositor), 0.218 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.447	α = 69.55
b = 51.038	β = 89.51
c = 59.12	γ = 77.63

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-06-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-06-26
Type: Initial release
Version 1.1: 2007-10-16
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2017-10-18
Changes: Advisory, Refinement description
Version 1.4: 2021-10-20
Changes: Advisory, Database references, Derived calculations
Version 1.5: 2023-08-30
Changes: Data collection, Refinement description

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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.