3KH1 | pdb_00003kh1

Crystal structure of Predicted metal-dependent phosphohydrolase (ZP_00055740.2) from Magnetospirillum magnetotacticum MS-1 at 1.37 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3KH1/pdb

• Classification: HYDROLASE
• Organism(s): Paramagnetospirillum magnetotacticum MS-1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-10-29 Released: 2009-11-24 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 
  0.164 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.132 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.133 (Depositor) 

Literature

Crystal structure of Predicted metal-dependent phosphohydrolase (ZP_00055740.2) from Magnetospirillum magnetotacticum MS-1 at 1.37 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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 45.78 kDa 
• Atom Count: 3,690 
• Modeled Residue Count: 385 
• Deposited Residue Count: 400 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Predicted metal-dependent phosphohydrolase	A, B	200	Paramagnetospirillum magnetotacticum MS-1	Mutation(s): 0  Gene Names: ZP_00055740.2
UniProt
Find proteins for D1MPT5 (Paramagnetospirillum magnetotacticum MS-1) Explore D1MPT5  Go to UniProtKB:  D1MPT5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	E [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-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: 1.37 Å
• R-Value Free:  0.164 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.132 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.133 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33KH1

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.852	α = 90
b = 83.906	β = 116.89
c = 71.278	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-24 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-11-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2017-10-25
  Changes: Advisory, Author supporting evidence, Database references, Polymer sequence, Refinement description, Source and taxonomy
• Version 2.1: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 2.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary