4HBZ | pdb_00004hbz

The Structure of Putative Phosphohistidine Phosphatase SixA from Nakamurella multipartitia.

• PDB DOI: https://doi.org/10.2210/pdb4HBZ/pdb

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


• Deposited: 2012-09-28 Released: 2012-10-17 
• Deposition Author(s): Cuff, M.E., Holowicki, J., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.161 (Depositor), 0.161 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.142 (Depositor) 

Literature

The Structure of Putative Phosphohistidine Phosphatase SixA from Nakamurella multipartitia.

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

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 19.7 kDa 
• Atom Count: 1,563 
• Modeled Residue Count: 172 
• Deposited Residue Count: 186 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative phosphohistidine phosphatase, SixA	A	186	Nakamurella multipartita DSM 44233	Mutation(s): 0  Gene Names: Namu_4970
UniProt
Find proteins for C8XA43 (Nakamurella multipartita (strain ATCC 700099 / DSM 44233 / CIP 104796 / JCM 9543 / NBRC 105858 / Y-104)) Explore C8XA43  Go to UniProtKB:  C8XA43

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	D [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL	C [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACY	B [auth A], F [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.161 (Depositor), 0.161 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.142 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.257	α = 90
b = 76.257	β = 90
c = 50.93	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-17 
Deposition Author(s): Cuff, M.E., Holowicki, J., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2012-10-17
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary