3K1M | pdb_00003k1m

Crystal Structure of full-length BenM, R156H mutant

PDB DOI: https://doi.org/10.2210/pdb3K1M/pdb

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

Deposited: 2009-09-28 Released: 2010-09-29
Deposition Author(s): Ruangprasert, A., Momany, C., Neidle, E.L., Craven, S.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free:
0.179 (Depositor), 0.239 (DCC)
R-Value Work:
0.147 (Depositor)
R-Value Observed:
0.148 (Depositor)

Starting Model: experimental
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This is version 1.4 of the entry. See complete history.

Literature

Structure of Full-length BenM

Ruangprasert, A., Craven, S.H., Neidle, E.L., Momany, C.

To be published.

Macromolecule Content

Total Structure Weight: 71.65 kDa
Atom Count: 5,429
Modeled Residue Count: 605
Deposited Residue Count: 624
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional regulator benM	A, B	312	Acinetobacter baylyi ADP1	Mutation(s): 1 Gene Names: ACIAD1435, benM, benR
UniProt
Find proteins for O68014 (Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)) Explore O68014 Go to UniProtKB: O68014
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O68014
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free: 0.179 (Depositor), 0.239 (DCC)
R-Value Work: 0.147 (Depositor)
R-Value Observed: 0.148 (Depositor)

Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.997	α = 90
b = 70.789	β = 90
c = 186.275	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-09-29

Deposition Author(s):

Ruangprasert, A.

Revision History (Full details and data files)

Version 1.0: 2010-09-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2021-10-13
Changes: Database references, Derived calculations
Version 1.4: 2023-09-06
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.