5DWD | pdb_00005dwd

Crystal structure of esterase PE8

PDB DOI: https://doi.org/10.2210/pdb5DWD/pdb

Classification: HYDROLASE
Organism(s): Pelagibacterium halotolerans B2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-09-22 Released: 2016-10-26
Deposition Author(s): Li, J., Huang, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free:
0.200 (Depositor), 0.207 (DCC)
R-Value Work:
0.156 (Depositor), 0.168 (DCC)
R-Value Observed:
0.158 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5DWD

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

Literature

Structure of esterase PE8

Li, J., Huang, J.

To be published.

Macromolecule Content

Total Structure Weight: 51.4 kDa
Atom Count: 3,579
Modeled Residue Count: 438
Deposited Residue Count: 480
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Esterase	A, B	240	Pelagibacterium halotolerans B2	Mutation(s): 0 Gene Names: KKY_2995 EC: 3.1.1.1
UniProt
Find proteins for G4RFI7 (Pelagibacterium halotolerans (strain DSM 22347 / JCM 15775 / CGMCC 1.7692 / B2)) Explore G4RFI7 Go to UniProtKB: G4RFI7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G4RFI7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PG Query on 1PG Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL C₁₁ H₂₄ O₆ SLNYBUIEAMRFSZ-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free: 0.200 (Depositor), 0.207 (DCC)
R-Value Work: 0.156 (Depositor), 0.168 (DCC)
R-Value Observed: 0.158 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.772	α = 90
b = 73.398	β = 102.37
c = 66.403	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-10-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-10-26
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.