4Y7D | pdb_00004y7d

Alpha/beta hydrolase fold protein from Nakamurella multipartita

• PDB DOI: https://doi.org/10.2210/pdb4Y7D/pdb

• Classification: HYDROLASE
• Organism(s): Nakamurella multipartita DSM 44233
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-02-14 Released: 2015-02-25 
• Deposition Author(s): Cuff, M.E., OSIPIUK, J., Holowicki, J., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 
  0.187 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Literature

Alpha/beta hydrolase fold protein from Nakamurella multipartita.

Cuff, M.E., OSIPIUK, J., Holowicki, J., Endres, M., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 64.23 kDa 
• Atom Count: 5,239 
• Modeled Residue Count: 577 
• Deposited Residue Count: 604 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha/beta hydrolase fold protein	A, B	302	Nakamurella multipartita DSM 44233	Mutation(s): 0  Gene Names: Namu_0557
UniProt
Find proteins for C8X7A4 (Nakamurella multipartita (strain ATCC 700099 / DSM 44233 / CIP 104796 / JCM 9543 / NBRC 105858 / Y-104)) Explore C8X7A4  Go to UniProtKB:  C8X7A4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free:  0.187 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34Y7D

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.404	α = 90
b = 75.394	β = 90
c = 126.536	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-02-25 
Deposition Author(s): Cuff, M.E., OSIPIUK, J., Holowicki, J., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM094585

Revision History  

• Version 1.0: 2015-02-25
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Advisory, Author supporting evidence, Derived calculations, Source and taxonomy, Structure summary
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary