4AC7

The crystal structure of Sporosarcina pasteurii urease in complex with citrate

Structural Biology Knowledgebase: 4AC7 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.146
  • R-Value Work: 0.117

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4AC7

Classification: HYDROLASE

Total Structure Weight: 88156.52

Macromolecule Entities
Molecule Chains Length Organism Details
UREASE SUBUNIT GAMMA A 100 Sporosarcina pasteurii EC#: 3.5.1.5 IUBMB
Gene Name(s): ureA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
UREASE SUBUNIT BETA B 126 Sporosarcina pasteurii EC#: 3.5.1.5 IUBMB
Gene Name(s): ureB
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
UREASE SUBUNIT ALPHA C 570 Sporosarcina pasteurii EC#: 3.5.1.5 IUBMB
Mutation: R19E, G28W, Y36T, Y37T, L38Y, V263L, M420I
Gene Name(s): ureC
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
FLC
Query on FLC

C CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

B, C SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, B, C 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NI
Query on NI

C NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OH
Query on OH

C HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
CXM
Query on CXM
A L-PEPTIDE LINKING C6 H11 N O4 S MET
KCX
Query on KCX
C L-PEPTIDE LINKING C7 H14 N2 O4 LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.146
  • R-Value Work: 0.117
  • Space Group: P 63 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 131.55 α = 90.00
b = 131.55 β = 90.00
c = 189.52 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-12-14
  • Released Date: 2013-01-16
  • Deposition author(s): Benini, S., Kosikowska, P., Cianci, M., Gonzalez Vara, A., Berlicki, L., Ciurli, S.

Revision History

  • 2014-12-03
    Type: Data collection | Details: REMARK 200
  • 2013-05-22
    Type: Citation | Details: REMARK 1, JRNL