6J6A | pdb_00006j6a

Crystal structure of TldE from Thermococcus kodakarensis

PDB DOI: https://doi.org/10.2210/pdb6J6A/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Thermococcus kodakarensis KOD1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-01-14 Released: 2020-01-15
Deposition Author(s): Zhang, X., Liu, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.228 (Depositor), 0.229 (DCC)
R-Value Work:
0.196 (Depositor), 0.197 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of TldE from Thermococcus kodakarensis

Zhang, X., Liu, J.

To be published.

Macromolecule Content

Total Structure Weight: 97.51 kDa
Atom Count: 7,110
Modeled Residue Count: 884
Deposited Residue Count: 886
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc-dependent protease, TldD/PmbA family	A, B	443	Thermococcus kodakarensis KOD1	Mutation(s): 0 Gene Names: TK0499
UniProt
Find proteins for Q5JD94 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JD94 Go to UniProtKB: Q5JD94
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JD94
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.228 (Depositor), 0.229 (DCC)
R-Value Work: 0.196 (Depositor), 0.197 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.497	α = 90
b = 104.497	β = 90
c = 253.927	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
ADSC	data collection
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-01-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-01-15
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-23
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.