5JD5 | pdb_00005jd5

Crystal structure of MGS-MilE3, an alpha/beta hydrolase enzyme from the metagenome of pyrene-phenanthrene enrichment culture with sediment sample of Milazzo Harbor, Italy

PDB DOI: https://doi.org/10.2210/pdb5JD5/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., Cui, H., Martinez-Martinez, M., Chernikova, T.N., Golyshin, P.N., Yakimov, M.M., Ferrer, M., Savchenko, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.237 (Depositor), 0.237 (DCC)
R-Value Work:
0.195 (Depositor), 0.196 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of MGS-MilE3, an alpha/beta hydrolase enzyme from the metagenome of pyrene-phenanthrene enrichment culture with sediment sample of Milazzo Harbor, Italy

Martinez-Martinez, M.

To be published.

Macromolecule Content

Total Structure Weight: 139.31 kDa
Atom Count: 11,745
Modeled Residue Count: 1,267
Deposited Residue Count: 1,284
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MGS-MilE3	A, B, C, D	321	uncultured bacterium	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OAS Query on OAS	A, B, C, D	L-PEPTIDE LINKING	C₅ H₉ N O₄		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.237 (Depositor), 0.237 (DCC)
R-Value Work: 0.195 (Depositor), 0.196 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.668	α = 90
b = 97.16	β = 90
c = 167.67	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-05-04

Deposition Author(s):

Martinez-Martinez, M.

Chernikova, T.N.

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
Version 1.2: 2024-10-16
Changes: 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.