5JD3

Crystal structure of LAE5, an alpha/beta hydrolase enzyme from the metagenome of Lake Arreo, Spain

PDB DOI: https://doi.org/10.2210/pdb5JD3/pdb

Classification: HYDROLASE
Organism(s): uncultured bacterium
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-04-15 Released: 2016-05-04
Deposition Author(s): Stogios, P.J., Xu, X., Nocek, B., Cui, H., Yim, V., Martinez-Martinez, M., Alcaide, M., Ferrer, M., Savchenko, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.236
R-Value Work: 0.184
R-Value Observed: 0.186

wwPDB Validation 3D Report Full Report

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

Literature

To be published

Martinez-Martinez, M.

To be published.

Macromolecule Content

Total Structure Weight: 214.78 kDa
Atom Count: 15,316
Modelled Residue Count: 1,743
Deposited Residue Count: 1,904
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LAE5	A, B, C, D, E A, B, C, D, E, F, G, H	238	uncultured bacterium	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth B] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B]	J [auth A], L [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth B] Interactions & Density Focus chain J [auth A] Focus chain L [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A]	K [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth C] SDF format, chain N [auth E] SDF format, chain O [auth H] MOL2 format, chain I [auth A] MOL2 format, chain M [auth C] MOL2 format, chain N [auth E] MOL2 format, chain O [auth H]	I [auth A], M [auth C], N [auth E], O [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain M [auth C] Focus chain N [auth E] Focus chain O [auth H] Interactions & Density Focus chain I [auth A] Focus chain M [auth C] Focus chain N [auth E] Focus chain O [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.236
R-Value Work: 0.184
R-Value Observed: 0.186
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.591	α = 90
b = 129.452	β = 97.49
c = 129.848	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	model building
Coot	model building
MrBUMP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2016-05-04

Deposition Author(s):

Martinez-Martinez, M.

Alcaide, M.

Ferrer, M.

Savchenko, A.

Revision History (Full details and data files)

Version 1.0: 2016-05-04
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description

Prepare Data

Validate Data

Deposit Data

Help and Resources

5JD3

Crystal structure of LAE5, an alpha/beta hydrolase enzyme from the metagenome of Lake Arreo, Spain

To be published

Entity ID: 1

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)