4Q9A | pdb_00004q9a

Crystal structure of a putative GDSL-like lipase (PARMER_00689) from Parabacteroides merdae ATCC 43184 at 2.86 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4Q9A/pdb

• Classification: HYDROLASE
• Organism(s): Parabacteroides merdae ATCC 43184
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-04-30 Released: 2014-06-25 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free: 
  0.232 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.182 (Depositor) 
• R-Value Observed: 
  0.185 (Depositor) 

Literature

Crystal structure of a putative GDSL-like lipase (PARMER_00689) from Parabacteroides merdae ATCC 43184 at 2.86 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 52.8 kDa 
• Atom Count: 3,509 
• Modeled Residue Count: 437 
• Deposited Residue Count: 458 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tat pathway signal sequence domain protein	A, B	229	Parabacteroides merdae ATCC 43184	Mutation(s): 0  Gene Names: PARMER_00689

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET
SEP	A, B	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free:  0.232 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.182 (Depositor) 
• R-Value Observed: 0.185 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34Q9A

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.829	α = 90
b = 128.829	β = 90
c = 149.65	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
BUSTER-TNT	refinement
XDS	data reduction
SHELXD	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-25 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2014-06-25
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.3: 2024-11-20
  Changes: Data collection, Structure summary