4JNN | pdb_00004jnn

Crystal structure of a putative transcriptional regulator from Saccharomonospora viridis in complex with benzamidine

• PDB DOI: https://doi.org/10.2210/pdb4JNN/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Saccharomonospora viridis DSM 43017
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-03-15 Released: 2013-04-10 
• Deposition Author(s): Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Endres, M., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.266 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a putative transcriptional regulator from Saccharomonospora viridis in complex with benzamidine

Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Endres, M., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

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: 23 kDa 
• Atom Count: 1,595 
• Modeled Residue Count: 191 
• Deposited Residue Count: 194 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator	A	194	Saccharomonospora viridis DSM 43017	Mutation(s): 0  Gene Names: Svir_16270
UniProt
Find proteins for C7MT25 (Saccharomonospora viridis (strain ATCC 15386 / DSM 43017 / JCM 3036 / CCUG 5913 / NBRC 12207 / NCIMB 9602 / P101)) Explore C7MT25  Go to UniProtKB:  C7MT25

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BEN	B [auth A]	BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N
BME	C [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-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: 2.35 Å
• R-Value Free:  0.266 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34JNN

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.791	α = 90
b = 109.952	β = 90
c = 76.875	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-10 
Deposition Author(s): Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Endres, M., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2013-04-10
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-12-06
  Changes: Data collection