3LHK | pdb_00003lhk

Crystal structure of putative DNA binding protein from Methanocaldococcus jannaschii.

PDB DOI: https://doi.org/10.2210/pdb3LHK/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Methanocaldococcus jannaschii DSM 2661
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-01-22 Released: 2010-02-02
Deposition Author(s): Chang, C., Chhor, G., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.249 (Depositor), 0.251 (DCC)
R-Value Work:
0.203 (Depositor), 0.215 (DCC)
R-Value Observed:
0.206 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3LHK

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of putative DNA binding protein from Methanocaldococcus jannaschii.

Chang, C., Chhor, G., Cobb, G., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 72.96 kDa
Atom Count: 5,040
Modeled Residue Count: 581
Deposited Residue Count: 616
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative DNA binding protein MJ0014	A, B, C, D	154	Methanocaldococcus jannaschii DSM 2661	Mutation(s): 0 Gene Names: MJ0014
UniProt
Find proteins for Q60329 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q60329 Go to UniProtKB: Q60329
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q60329
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.249 (Depositor), 0.251 (DCC)
R-Value Work: 0.203 (Depositor), 0.215 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.349	α = 90
b = 86.16	β = 90
c = 115.464	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	model building
RESOLVE	model building
Coot	model building
ARP/wARP	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-02-02

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2010-02-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, 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.