5NEZ | pdb_00005nez

crystal structure of variants

PDB DOI: https://doi.org/10.2210/pdb5NEZ/pdb

Classification: TRANSFERASE
Organism(s): Methanothermobacter thermautotrophicus str. Delta H
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-03-13 Released: 2018-05-16
Deposition Author(s): Linde, M., Rajendran, C., Babinger, P., Sterner, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free:
0.230 (Depositor), 0.234 (DCC)
R-Value Work:
0.176 (Depositor), 0.185 (DCC)
R-Value Observed:
0.179 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5NEZ

This is version 1.1 of the entry. See complete history.

Literature

crystal structure of variants from MtGGGPS

Sterner, R., Babinger, P., Linde, M., Rajendran, C.

To be published.

Macromolecule Content

Total Structure Weight: 165.82 kDa
Atom Count: 11,054
Modeled Residue Count: 1,445
Deposited Residue Count: 1,536
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Geranylgeranylglyceryl phosphate synthase	A, B, C, D, E A, B, C, D, E, F	256	Methanothermobacter thermautotrophicus str. Delta H	Mutation(s): 0 Gene Names: MTH_552 EC: 2.5.1.41
UniProt
Find proteins for O26652 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O26652 Go to UniProtKB: O26652
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O26652
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free: 0.230 (Depositor), 0.234 (DCC)
R-Value Work: 0.176 (Depositor), 0.185 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.978	α = 90
b = 136.409	β = 90
c = 152.503	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-05-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-05-16
Type: Initial release
Version 1.1: 2024-05-08
Changes: Data collection, Database references

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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.