6K34 | pdb_00006k34

Crystal Structure of DphMB1

PDB DOI: https://doi.org/10.2210/pdb6K34/pdb

Classification: HYDROLASE
Organism(s): Mycobacterium adipatum
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2019-05-16 Released: 2020-06-03
Deposition Author(s): Fan, S.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.253 (Depositor), 0.253 (DCC)
R-Value Work:
0.187 (Depositor), 0.188 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of DphMB1

Fan, S.

To be published.

Macromolecule Content

Total Structure Weight: 135.58 kDa
Atom Count: 9,181
Modeled Residue Count: 1,204
Deposited Residue Count: 1,280
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipase	A [auth B], B [auth A], C, D	320	Mycobacterium adipatum	Mutation(s): 0 Gene Names: A7U43_17735, dphMB1
UniProt
Find proteins for A0A172UPQ1 (Mycobacterium adipatum) Explore A0A172UPQ1 Go to UniProtKB: A0A172UPQ1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A172UPQ1
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.253 (Depositor), 0.253 (DCC)
R-Value Work: 0.187 (Depositor), 0.188 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.575	α = 90
b = 159.539	β = 105.09
c = 71.132	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-06-03

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31170119

Revision History (Full details and data files)

Version 1.0: 2020-06-03
Type: Initial release
Version 1.1: 2023-11-22
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.