3GO4 | pdb_00003go4

Crystal structure of a duf574 family protein (sav_2177) from streptomyces avermitilis ma-4680 at 1.80 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3GO4/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Streptomyces avermitilis MA-4680 = NBRC 14893
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-18 Released: 2009-04-14 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.250 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Rossmann-fold protein of unknown function (DUF574) (NP_823353.1) from Streptomyces avermitilis MA-4680 at 1.80 A resolution

Joint Center for Structural Genomics (JCSG)

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: 31.24 kDa 
• Atom Count: 2,299 
• Modeled Residue Count: 262 
• Deposited Residue Count: 277 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein of unknown function DUF574	A	277	Streptomyces avermitilis MA-4680 = NBRC 14893	Mutation(s): 0  Gene Names: NP_823353.1, SAV2177, SAV_2177
UniProt
Find proteins for Q82L35 (Streptomyces avermitilis (strain ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680)) Explore Q82L35  Go to UniProtKB:  Q82L35

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	B [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-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: 1.80 Å
• R-Value Free:  0.250 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33GO4

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.637	α = 90
b = 49.439	β = 123.8
c = 77.811	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-14 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-04-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2023-09-20
  Changes: Data collection, Refinement description
• Version 1.6: 2023-11-22
  Changes: Data collection
• Version 1.7: 2024-11-06
  Changes: Data collection, Structure summary