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- PDB-1gmw: Structure of UreE -

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Basic information

Entry
Database: PDB / ID: 1gmw
TitleStructure of UreE
Components(UREE) x 2
KeywordsCHAPERONE / METALLOCHAPERONE
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
COPPER (II) ION / Urease accessory protein UreE
Similarity search - Component
Biological speciesKLEBSIELLA AEROGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,06610
Polymers63,6844
Non-polymers3816
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-46.7 kcal/mol
Surface area33180 Å2
MethodPQS
Unit cell
Length a, b, c (Å)43.756, 129.905, 56.419
Angle α, β, γ (deg.)90.00, 91.21, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99886, 0.03958, -0.02668), (-0.03682, -0.9946, -0.097), (-0.03038, -0.09591, 0.99493)21.89391, 72.7948, 4.35899
2given(0.87653, 0.40629, 0.25811), (0.43457, -0.89854, -0.06139), (0.20698, 0.16598, -0.96416)-3.24618, 29.38293, -28.22077
3given(-0.88484, -0.41246, -0.21663), (-0.43377, 0.89902, 0.06005), (0.16999, 0.1471, -0.9744)26.16558, 43.47604, -25.28455

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Components

#1: Protein UREE


Mass: 15924.580 Da / Num. of mol.: 3 / 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: Protein UREE


Mass: 15910.553 Da / Num. of mol.: 1 / 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
#3: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION: CHAINS A,D ALA(91)HIS CHAIN D ASP(63)GLU
Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51.14 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mMTris-HCl1droppH7.5
220 mMimidazole1drop
32 mMEDTA1drop
42 mMdithiothreitol1drop
515 mg/mlprotein1drop
6100 mMsodium cacodylate1reservoirpH6.5
718-19 %(w/v)PEG80001reservoir
8200 mMcalcium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.5→17 Å / Num. obs: 20709 / % possible obs: 97.5 % / Redundancy: 19 % / Rmerge(I) obs: 0.048
Reflection
*PLUS
Num. measured all: 198257
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.54 Å / % possible obs: 99.2 % / Rmerge(I) obs: 0.088

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Processing

SoftwareName: CNS / Version: 1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / 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. atoms4263 0 6 164 4433
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
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 17 Å / Num. reflection obs: 20352 / Rfactor Rfree: 0.295
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.36

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