6ZL7 | pdb_00006zl7

CRYSTAL STRUCTURE OF C173S MUTATION IN THE PMGL2 ESTERASE FROM PERMAFROST METAGENOMIC LIBRARY

PDB DOI: https://doi.org/10.2210/pdb6ZL7/pdb

Classification: HYDROLASE
Organism(s): uncultured bacterium
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-06-30 Released: 2020-07-08
Deposition Author(s): Goryaynova, D.A., Boyko, K.M., Nikolaeva, A.Y., Korzhenevskiy, D.A., Kryukova, M.V., Petrovskaya, L.E., Novototskaya-Vlasova, K.A., Rivkina, E.M., Dolgikh, D.A., Kirpichnikov, M.P., Popov, V.O.
Funding Organization(s): Russian Foundation for Basic Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.196 (Depositor), 0.196 (DCC)
R-Value Work:
0.169 (Depositor), 0.169 (DCC)
R-Value Observed:
0.170 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

CRYSTAL STRUCTURE OF C173S MUTATION IN THE PMGL2 ESTERASE FROM PERMAFROST METAGENOMIC LIBRARY

Goryaynova, D.A., Boyko, K.M., Nikolaeva, A.Y., Korzhenevskiy, D.A., Kryukova, M.V., Petrovskaya, L.E., Novototskaya-Vlasova, K.A., Rivkina, E.M., Dolgikh, D.A., Kirpichnikov, M.P., Popov, V.O.

To be published.

Macromolecule Content

Total Structure Weight: 75.65 kDa
Atom Count: 5,284
Modeled Residue Count: 637
Deposited Residue Count: 702
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PMGL2	A, B	351	uncultured bacterium	Mutation(s): 1 EC: 3.1.1.3
UniProt
Find proteins for A0ACD6B8V3 (uncultured bacterium) Explore A0ACD6B8V3 Go to UniProtKB: A0ACD6B8V3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B8V3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG6 Query on PG6 Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth B]	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE C₁₂ H₂₆ O₆ DMDPGPKXQDIQQG-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.196 (Depositor), 0.196 (DCC)
R-Value Work: 0.169 (Depositor), 0.169 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.149	α = 90
b = 92.53	β = 106.61
c = 74.41	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-07-08

Deposition Author(s):

Goryaynova, D.A.

Nikolaeva, A.Y.

Korzhenevskiy, D.A.

Petrovskaya, L.E.

Novototskaya-Vlasova, K.A.

Kirpichnikov, M.P.

Funding Organization	Location	Grant Number
Russian Foundation for Basic Research	Russian Federation	18-04-00491

Revision History (Full details and data files)

Version 1.0: 2020-07-08
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Database references, Refinement description

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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.