4PSU | pdb_00004psu

Crystal structure of alpha/beta hydrolase from Rhodopseudomonas palustris CGA009

PDB DOI: https://doi.org/10.2210/pdb4PSU/pdb

Classification: HYDROLASE
Organism(s): Rhodopseudomonas palustris CGA009
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-03-07 Released: 2015-03-11
Deposition Author(s): Nocek, B., Hajighasemi, M., Xu, X., Cui, H., Savchenko, A., Yakunin, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.221 (Depositor), 0.228 (DCC)
R-Value Work:
0.181 (Depositor), 0.187 (DCC)
R-Value Observed:
0.183 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4PSU

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

Literature

Crystal structure of alpha/beta hydrolase from Rhodopseudomonas palustris CGA009

Nocek, B., Hajighasemi, M., Xu, X., Cui, H., Savchenko, A., Yakunin, A.

To be published.

Macromolecule Content

Total Structure Weight: 32.73 kDa
Atom Count: 2,234
Modeled Residue Count: 286
Deposited Residue Count: 295
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha/beta hydrolase	A	295	Rhodopseudomonas palustris CGA009	Mutation(s): 0 Gene Names: RPA1511 EC: 3
UniProt
Find proteins for Q6N9M9 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6N9M9 Go to UniProtKB: Q6N9M9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6N9M9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
12P Query on 12P Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	DODECAETHYLENE GLYCOL C₂₄ H₅₀ O₁₃ WRZXKWFJEFFURH-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	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: 0.221 (Depositor), 0.228 (DCC)
R-Value Work: 0.181 (Depositor), 0.187 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.013	α = 90
b = 87.425	β = 90
c = 93.702	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
MLPHARE	phasing
DM	model building
ARP/wARP	model building
CCP4	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
CCP4	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-03-11

Deposition Author(s):

Hajighasemi, M.

Revision History (Full details and data files)

Version 1.0: 2015-03-11
Type: Initial release
Version 1.1: 2024-11-06
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.