4CU4

FhuA from E. coli in complex with the lasso peptide microcin J25 (MccJ25)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FERRICHROME-IRON RECEPTOR706Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P06971 (Escherichia coli (strain K12))
Explore P06971 
Go to UniProtKB:  P06971
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06971
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MICROCIN J2521Escherichia coli str. K-12 substr. MC4100Mutation(s): 0 
UniProt
Find proteins for Q9X2V7 (Escherichia coli)
Explore Q9X2V7 
Go to UniProtKB:  Q9X2V7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X2V7
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
L-glycero-alpha-D-manno-heptopyranose-(1-3)-L-glycero-alpha-D-manno-heptopyranose-(1-5)-[3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)]3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-alpha-D-glucopyranose
C
6N/A
Glycosylation Resources
GlyTouCan:  G23424DU
GlyCosmos:  G23424DU
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3PH
Query on 3PH

Download Ideal Coordinates CCD File 
BA [auth A]1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
FTT
Query on FTT

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D [auth A],
E [auth A],
F [auth A],
H [auth A]
3-HYDROXY-TETRADECANOIC ACID
C14 H28 O3
ATRNZOYKSNPPBF-CYBMUJFWSA-N
LDA
Query on LDA

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AA [auth A]
CA [auth A]
DA [auth A]
J [auth A]
K [auth A]
AA [auth A],
CA [auth A],
DA [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
MYR
Query on MYR

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I [auth A]MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
DAO
Query on DAO

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G [auth A]LAURIC ACID
C12 H24 O2
POULHZVOKOAJMA-UHFFFAOYSA-N
DPO
Query on DPO

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EA [auth A],
GA [auth A]
DIPHOSPHATE
O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-J
PO4
Query on PO4

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FA [auth A],
HA [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.98α = 90
b = 277.05β = 90
c = 106.76γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
xia2data reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 1.1: 2014-04-16
    Changes: Database references
  • Version 1.2: 2014-04-30
    Changes: Database references
  • Version 1.3: 2018-06-13
    Changes: Data collection, Structure summary
  • Version 1.4: 2019-07-31
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.5: 2020-07-01
    Changes: Data collection, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary