3VNR | pdb_00003vnr

Co-crystal structure of NRPS adenylation protein CytC1 with aminobutyric acid and AMP from streptomyces

• PDB DOI: https://doi.org/10.2210/pdb3VNR/pdb

• Classification: LIGASE
• Organism(s): Streptomyces sp.
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-01-17 Released: 2013-01-23 
• Deposition Author(s): Okumura, H., Ueki, M., Shiro, Y., Osada, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Substrate recognition mechanism of NRPS adenylation protein from Streptomyces

Ueki, M., Okumura, H., Osada, H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 59.44 kDa 
• Atom Count: 4,135 
• Modeled Residue Count: 493 
• Deposited Residue Count: 544 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NRPS adenylation protein CytC1	A	544	Streptomyces sp.	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	B [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
ABA	C [auth A]	ALPHA-AMINOBUTYRIC ACID C4 H9 N O2 QWCKQJZIFLGMSD-VKHMYHEASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.016	α = 90
b = 157.016	β = 90
c = 157.016	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
BSS	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-23 
Deposition Author(s): Okumura, H., Ueki, M., Shiro, Y., Osada, H.

Revision History  

• Version 1.0: 2013-01-23
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-12-06
  Changes: Data collection