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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of DphMB1

Fan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

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

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.190 (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

Entry History & Funding Information

Deposition Data

• Released Date: 2020-06-03 
Deposition Author(s): Fan, S.

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

Revision History  

• Version 1.0: 2020-06-03
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description