6QVM | pdb_00006qvm

Undecaheme cytochrome from S-layer of Carboxydothermus ferrireducens


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.210 (Depositor), 0.180 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HECClick on this verticalbar to view details

This is version 2.2 of the entry. See complete history


Literature

Extracellular Fe(III) reductase structure reveals a modular organization enabling S-layer insertion and electron transfer to insoluble substrates

Tikhonova, T.V.Osipov, E.M.Dergousova, N.I.Boyko, K.M.Elizarov, I.M.Gavrilov, S.N.Khrenova, M.G.Robb, F.T.Solovieva, A.Y.Bonch-Osmolovskaya, E.A.Popov, V.O.

(2023) Structure 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Multiheme cytochrome cf681Carboxydothermus ferrireducens DSM 11255Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose
B, C
2N/A
Glycosylation Resources
GlyTouCan:  G50538IF
GlyCosmos:  G50538IF
GlyGen:  G50538IF
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose
D
3N/A
Glycosylation Resources
GlyTouCan:  G03505DU
GlyCosmos:  G03505DU
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
P [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
PO4
Query on PO4

Download Ideal Coordinates CCD File 
T [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
Q [auth A],
R [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
S [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.210 (Depositor), 0.180 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.679α = 90
b = 193.98β = 90
c = 170.779γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
iMOSFLMdata reduction
Aimlessdata scaling
AutoSolphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HECClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Science FoundationRussian Federation14-24-00172

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-25
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-02-08
    Changes: Database references, Derived calculations, Structure summary
  • Version 2.2: 2024-11-13
    Changes: Data collection, Structure summary