3QKC | pdb_00003qkc

CRYSTAL STRUCTURE OF geranyl diphosphate synthase small subunit from Antirrhinum majus

PDB DOI: https://doi.org/10.2210/pdb3QKC/pdb

Classification: TRANSFERASE
Organism(s): Antirrhinum majus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-01-31 Released: 2011-02-16
Deposition Author(s): Malashkevich, V.N., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.289 (Depositor), 0.290 (DCC)
R-Value Work:
0.209 (Depositor), 0.209 (DCC)
R-Value Observed:
0.213 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of geranyl diphosphate synthase small subunit from Antirrhinum majus

Malashkevich, V.N., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 60 kDa
Atom Count: 3,997
Modeled Residue Count: 512
Deposited Residue Count: 546
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Geranyl diphosphate synthase small subunit	A [auth B], B [auth A]	273	Antirrhinum majus	Mutation(s): 0 Gene Names: AAS82859 EC: 2.5.1.1
UniProt
Find proteins for Q6QLV2 (Antirrhinum majus) Explore Q6QLV2 Go to UniProtKB: Q6QLV2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6QLV2
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.289 (Depositor), 0.290 (DCC)
R-Value Work: 0.209 (Depositor), 0.209 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.199	α = 66.69
b = 48.789	β = 89.28
c = 61.593	γ = 89.98

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-02-16

Deposition Author(s):

Malashkevich, V.N.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2011-02-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2018-11-21
Changes: Data collection, Structure summary
Version 1.3: 2021-02-10
Changes: Database references, Structure summary
Version 1.4: 2024-02-21
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.