4RNC | pdb_00004rnc

Crystal structure of an esterase RhEst1 from Rhodococcus sp. ECU1013

PDB DOI: https://doi.org/10.2210/pdb4RNC/pdb

Classification: HYDROLASE
Organism(s): Rhodococcus sp. ECU1013
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-10-23 Released: 2015-10-28
Deposition Author(s): Dou, S., Kong, X.D., Xu, J.H., Zhou, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.212 (Depositor), 0.223 (DCC)
R-Value Work:
0.161 (Depositor), 0.171 (DCC)
R-Value Observed:
0.164 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4RNC

This is version 1.2 of the entry. See complete history.

Literature

Substrate channel evolution of an esterase for the synthesis of Cilastatin

Luan, Z.J., L Li, F., Dou, S., Chen, Q., Kong, X.D., Zhou, J., Yu, H.L., Xu, J.H.

(2015) Catal Sci Technol 5: 2622-2629

Macromolecule Content

Total Structure Weight: 97.58 kDa
Atom Count: 6,672
Modeled Residue Count: 831
Deposited Residue Count: 930
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Esterase	A, B, C	310	Rhodococcus sp. ECU1013	Mutation(s): 0 EC: 3.1.1.1
UniProt
Find proteins for A0A088CB91 (Rhodococcus sp. ECU1013) Explore A0A088CB91 Go to UniProtKB: A0A088CB91
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A088CB91
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain E [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth C] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth C] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth B], F [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.212 (Depositor), 0.223 (DCC)
R-Value Work: 0.161 (Depositor), 0.171 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 212.926	α = 90
b = 45.383	β = 105.82
c = 77.443	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASES	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-10-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-10-28
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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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.