3CR7 | pdb_00003cr7

Crystal structure of N-terminal truncation of APS Kinase from Penicillium chrysogenum: Ternary structure with ADP and PAPS

• PDB DOI: https://doi.org/10.2210/pdb3CR7/pdb

• Classification: TRANSFERASE
• Organism(s): Penicillium chrysogenum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-04-04 Released: 2009-02-17 
• Deposition Author(s): Gay, S.C., Segel, I.H., Fisher, A.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.279 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Truncated APS kinase from Pencillium chrysogenum: Insight into the function of the N-terminal helix

Gay, S.C., Segel, I.H., Fisher, A.J.

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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 92.25 kDa 
• Atom Count: 6,230 
• Modeled Residue Count: 721 
• Deposited Residue Count: 788 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylyl-sulfate kinase	A, B, C, D	197	Penicillium chrysogenum	Mutation(s): 0  EC: 2.7.1.25
UniProt
Find proteins for Q12657 (Penicillium chrysogenum) Explore Q12657  Go to UniProtKB:  Q12657

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PPS	G [auth A], L [auth C]	3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE C10 H15 N5 O13 P2 S GACDQMDRPRGCTN-KQYNXXCUSA-N
ADP	F [auth A], I [auth B], K [auth C], M [auth D]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
CL	E [auth A], H [auth B], J [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.279 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.58	α = 90
b = 82.594	β = 90
c = 139.009	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
EPMR	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-17 
Deposition Author(s): Gay, S.C., Segel, I.H., Fisher, A.J.

Revision History  

• Version 1.0: 2009-02-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description