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- PDB-1gmu: Structure of UreE -

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Basic information

Entry
Database: PDB / ID: 1gmu
TitleStructure of UreE
ComponentsUREE
KeywordsMETALLOCHAPERONE
Function / homology
Function and homology information


urea metabolic process / nickel cation binding / unfolded protein binding / protein folding / protein-containing complex assembly / cytoplasm
Similarity search - Function
UreE urease accessory, N-terminal / Urease accessory protein UreE, C-terminal domain / Urease accessory protein UreE / UreE urease accessory, N-terminal domain superfamily / UreE urease accessory protein, N-terminal domain / UreE urease accessory protein, C-terminal domain / UreE urease accessory protein, N-terminal domain / UreE, C-terminal domain / Urease metallochaperone UreE, N-terminal domain / HSP40/DNAj peptide-binding domain ...UreE urease accessory, N-terminal / Urease accessory protein UreE, C-terminal domain / Urease accessory protein UreE / UreE urease accessory, N-terminal domain superfamily / UreE urease accessory protein, N-terminal domain / UreE urease accessory protein, C-terminal domain / UreE urease accessory protein, N-terminal domain / UreE, C-terminal domain / Urease metallochaperone UreE, N-terminal domain / HSP40/DNAj peptide-binding domain / Alpha-Beta Plaits / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Urease accessory protein UreE
Similarity search - Component
Biological speciesKLEBSIELLA AEROGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsSong, H.K. / Mulrooney, S.B. / Huber, R. / Hausinger, R.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Crystal Structure of Klebsiella Aerogenes Uree, a Nickel-Binding Metallochaperone for Urease Activation.
Authors: Song, H.K. / Mulrooney, S.B. / Huber, R. / Hausinger, R.
History
DepositionSep 24, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UREE
B: UREE
C: UREE
D: UREE


Theoretical massNumber of molelcules
Total (without water)62,9484
Polymers62,9484
Non-polymers00
Water17,330962
1
A: UREE


Theoretical massNumber of molelcules
Total (without water)15,7371
Polymers15,7371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: UREE


Theoretical massNumber of molelcules
Total (without water)15,7371
Polymers15,7371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: UREE


Theoretical massNumber of molelcules
Total (without water)15,7371
Polymers15,7371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: UREE


Theoretical massNumber of molelcules
Total (without water)15,7371
Polymers15,7371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)43.882, 129.360, 56.786
Angle α, β, γ (deg.)90.00, 93.72, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99623, 0.00464, -0.08663), (0.00059, -0.99819, -0.06018), (-0.08676, -0.06001, 0.99442)24.18361, 72.34355, 3.42209
2given(0.86046, 0.42849, 0.27569), (0.45499, -0.88971, -0.03727), (0.22931, 0.15751, -0.96052)-6.10036, 29.33323, 27.63065
3given(-0.83951, -0.5132, -0.51866), (0.85478, -0.0184, -0.17834), (0.16188, 0.07705, -0.9838)26.42195, 44.57207, 30.7321

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Components

#1: Protein
UREE


Mass: 15736.998 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-143 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) KLEBSIELLA AEROGENES (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P18317
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 962 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.86 %
Crystal growpH: 6.5 / Details: pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.0500, 0.9500, 0.9815, 0.9805
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.051
20.951
30.98151
40.98051
ReflectionResolution: 1.5→17 Å / Num. obs: 97562 / % possible obs: 96.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.026

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Processing

SoftwareName: CNS / Version: 1 / Classification: refinement
RefinementMethod to determine structure: MAD / Resolution: 1.5→17 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.261 9152 10 %RANDOM
Rwork0.223 ---
obs0.223 91545 91 %-
Refinement stepCycle: LAST / Resolution: 1.5→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4281 0 0 962 5243
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004631
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.30162
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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