3K6K

Crystal structure at 2.2 angstrom of HSL-homolog EstE7 from a metagenome library

PDB DOI: https://doi.org/10.2210/pdb3K6K/pdb

Classification: HYDROLASE
Organism(s): uncultured bacterium
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2009-10-09 Released: 2009-10-27
Deposition Author(s): Hwang, K.Y., Nam, K.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.282 (Depositor), 0.280 (DCC)
R-Value Work:
0.223 (Depositor), 0.220 (DCC)
R-Value Observed:
0.226 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Biochemical and structural analysis of hormone-sensitive lipase homolog EstE7; Insight into the stabilized dimerization of HSL-homolog proteins

Nam, K.H., Rhee, K.H., Lee, W.H., Jeong, B.-C., Song, H.K., Hwang, K.Y.

To be published.

Macromolecule Content

Total Structure Weight: 139.56 kDa
Atom Count: 9,335
Modelled Residue Count: 1,177
Deposited Residue Count: 1,288
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Esterase/lipase	A, B, C, D	322	uncultured bacterium	Mutation(s): 0 Gene Names: estE7 EC: 3.1.1
UniProt
Find proteins for Q0GMU1 (uncultured bacterium) Explore Q0GMU1 Go to UniProtKB: Q0GMU1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q0GMU1
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain L [auth D] SDF format, chain M [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain L [auth D] mmCIF format, chain M [auth D]	E [auth A] F [auth A] G [auth B] H [auth B] I [auth B] E [auth A], F [auth A], G [auth B], H [auth B], I [auth B], J [auth C], K [auth C], L [auth D], M [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth D]
BME Query on BME Download Ideal Coordinates CCD File SDF format, chain N [auth D] MOL2 format, chain N [auth D] mmCIF format, chain N [auth D]	N [auth D]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain N [auth D] Interactions & Density Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.282 (Depositor), 0.280 (DCC)
R-Value Work: 0.223 (Depositor), 0.220 (DCC)
R-Value Observed: 0.226 (Depositor)

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.157	α = 90
b = 127.699	β = 90
c = 232.87	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-10-27

Deposition Author(s):

Hwang, K.Y.

Nam, K.H.

Revision History (Full details and data files)

Version 1.0: 2009-10-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description