3RMS

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free:
0.205 (Depositor), 0.200 (DCC)
R-Value Work:
0.177 (Depositor), 0.170 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C7MVX3
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain L [auth C] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C]	E [auth A] G [auth B] H [auth B] I [auth B] J [auth B] 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		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] SDF format, chain K [auth C] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain K [auth C] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain K [auth C]	D [auth A], F [auth B], K [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain K [auth C] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain K [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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), 0.200 (DCC)
R-Value Work: 0.177 (Depositor), 0.170 (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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-05-11

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

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