3RMS | pdb_00003rms

Crystal structure of uncharacterized protein Svir_20580 from Saccharomonospora viridis

• PDB DOI: https://doi.org/10.2210/pdb3RMS/pdb

• Classification: Structural Genomics, unknown function
• Organism(s): Saccharomonospora viridis DSM 43017
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• 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: 2.13 Å
• R-Value Free: 
  0.205 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of uncharacterized protein Svir_20580 from Saccharomonospora viridis

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)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 39.82 kDa 
• Atom Count: 2,686 
• Modeled Residue Count: 327 
• Deposited Residue Count: 348 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein	A, B, C	116	Saccharomonospora viridis DSM 43017	Mutation(s): 0  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], G [auth B], H [auth B], I [auth B], J [auth B], L [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	D [auth A], F [auth B], K [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free:  0.205 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.63	α = 90
b = 60.968	β = 96.77
c = 73.209	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
PHASER	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

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: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-12-06
  Changes: Data collection
• Version 1.4: 2024-11-27
  Changes: Structure summary