3RMQ | pdb_00003rmq

Crystal structure of uncharacterized protein Svir_20580 from Saccharomonospora viridis (V71M mutant)

• PDB DOI: https://doi.org/10.2210/pdb3RMQ/pdb

• Classification: Structural Genomics, unknown function
• Organism(s): Saccharomonospora viridis DSM 43017
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2011-04-21 Released: 2011-05-11 
• Deposition Author(s): Michalska, K., Weger, A., Hatzos-Skintges, C., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.191 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Literature

Crystal structure of uncharacterized protein Svir_20580 from Saccharomonospora viridis (V71M mutant)

Michalska, K., Weger, A., Hatzos-Skintges, C., Bearden, J., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 13.54 kDa 
• Atom Count: 999 
• Modeled Residue Count: 111 
• Deposited Residue Count: 116 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein	A	116	Saccharomonospora viridis DSM 43017	Mutation(s): 1  Gene Names: Svir_20580
UniProt
Find proteins for C7MVX3 (Saccharomonospora viridis (strain ATCC 15386 / DSM 43017 / JCM 3036 / CCUG 5913 / NBRC 12207 / NCIMB 9602 / P101)) Explore C7MVX3  Go to UniProtKB:  C7MVX3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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: 1.85 Å
• R-Value Free:  0.191 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.225	α = 90
b = 79.225	β = 90
c = 47.051	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-11 
Deposition Author(s): Michalska, K., Weger, A., Hatzos-Skintges, C., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2011-05-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary