3HDT | pdb_00003hdt

Crystal structure of putative kinase from Clostridium symbiosum ATCC 14940

• PDB DOI: https://doi.org/10.2210/pdb3HDT/pdb

• Classification: structural genomics, unknown function
• Organism(s): [Clostridium] symbiosum ATCC 14940
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-05-07 Released: 2009-05-26 
• Deposition Author(s): Chang, C., Freeman, L., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free: 
  0.276 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Literature

Crystal structure of putative kinase from Clostridium symbiosum ATCC 14940

Chang, C., Freeman, L., Jedrzejczak, R., Joachimiak, A.

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: 52.49 kDa 
• Atom Count: 2,761 
• Modeled Residue Count: 338 
• Deposited Residue Count: 446 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative kinase	A, B	223	[Clostridium] symbiosum ATCC 14940	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], E [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL	D [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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: 2.79 Å
• R-Value Free:  0.276 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.443	α = 90
b = 95.443	β = 90
c = 109.375	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
RESOLVE	model building
ARP/wARP	model building
Coot	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-26 
Deposition Author(s): Chang, C., Freeman, L., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-05-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary