5UUS | pdb_00005uus

SrtF sortase from Corynebacterium diphtheriae

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 
    0.191 (Depositor), 0.198 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5UUS

This is version 1.5 of the entry. See complete history. 

Literature

Macromolecule Content 

  • Total Structure Weight: 50.99 kDa 
  • Atom Count: 3,387 
  • Modeled Residue Count: 413 
  • Deposited Residue Count: 458 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Possible sortase-like protein
A, B
229Corynebacterium diphtheriae NCTC 13129Mutation(s): 0 
Gene Names: DIP2272
UniProt
Find proteins for Q6NEK1 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis))
Explore Q6NEK1 
Go to UniProtKB:  Q6NEK1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6NEK1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPD

Query on MPD


Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
I [auth B],
J [auth B]		(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
EDO

Query on EDO


Download:Ideal Coordinates CCD File
G [auth A],
M [auth B]		1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT

Query on ACT


Download:Ideal Coordinates CCD File
F [auth A],
L [auth B]		ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
FMT

Query on FMT


Download:Ideal Coordinates CCD File
H [auth A]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
CL

Query on CL


Download:Ideal Coordinates CCD File
E [auth A],
K [auth B]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A, B
L-PEPTIDE LINKINGC3 H7 N O3 SCYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free:  0.191 (Depositor), 0.198 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.99α = 90
b = 69.99β = 90
c = 237.292γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data scaling
HKL-3000data reduction
HKL-3000phasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272200700058C
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201200026C

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Author supporting evidence, Refinement description
  • Version 1.2: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2023-11-15
    Changes: Data collection
  • Version 1.5: 2024-10-09
    Changes: Structure summary