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- PDB-1ear: Crystal structure of Bacillus pasteurii UreE at 1.7 A. Type II cr... -

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Basic information

Entry
Database: PDB / ID: 1ear
TitleCrystal structure of Bacillus pasteurii UreE at 1.7 A. Type II crystal form.
ComponentsUREASE ACCESSORY PROTEIN UREE
KeywordsCHAPERONE / PUTATIVE NI-CHAPERONE / UREASE OPERON
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 speciesBACILLUS PASTEURII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsRemaut, H. / Safarov, N. / Ciurli, S. / Van Beeumen, J.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Structural Basis for Ni2+ Transport and Assembly of the Urease Active Site by the Metallochaperone Uree from Bacillus Pasteurii
Authors: Reamut, H. / Safarov, N. / Ciurli, S. / Van Beeumen, J.
History
DepositionJul 16, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 4, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 27, 2018Group: Data collection / Derived calculations
Category: diffrn_source / pdbx_struct_conn_angle / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.7Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
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

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Assembly

Deposited unit
A: UREASE ACCESSORY PROTEIN UREE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4782
Polymers17,4131
Non-polymers651
Water2,306128
1
A: UREASE ACCESSORY PROTEIN UREE
hetero molecules

A: UREASE ACCESSORY PROTEIN UREE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9574
Polymers34,8262
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)44.320, 63.510, 129.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1143-

ZN

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Components

#1: Protein UREASE ACCESSORY PROTEIN UREE


Mass: 17412.934 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: PUTATIVE NI-CHAPERONE / Source: (gene. exp.) BACILLUS PASTEURII (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P50049
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 294 K / pH: 7 / Details: 92-96 % NACITRATE, 100MM TRIS PH 7, 294 K
Crystal grow
*PLUS
Temperature: 294 K / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
250 mMTris-HCl1droppH7.5
3100 mM1dropNaCl
486-92 %citrate1reservoir
5100 mMTris-HCl1reservoirpH7.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8453
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8453 Å / Relative weight: 1
ReflectionResolution: 1.7→15 Å / Num. obs: 20619 / % possible obs: 99 % / Redundancy: 6.2 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 32.6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 3.63 / % possible all: 96.8
Reflection
*PLUS
Num. measured all: 292340
Reflection shell
*PLUS
% possible obs: 96.8 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB IDCODE 1EB0

1eb0


Resolution: 1.7→14.85 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.7
Details: B-FACTOR WAS FIXED AT 100 A**2 FOR DISORDERED SIDECHAINS
RfactorNum. reflection% reflectionSelection details
Rfree0.2281 1037 5.1 %RANDOM
Rwork0.2126 ---
obs0.2126 20288 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.8566 Å2 / ksol: 0.416487 e/Å3
Displacement parametersBiso mean: 33.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.63 Å20 Å20 Å2
2---4.1 Å20 Å2
3---6.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.7→14.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1176 0 1 128 1305
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.62
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.751.5
X-RAY DIFFRACTIONc_mcangle_it3.962
X-RAY DIFFRACTIONc_scbond_it5.632
X-RAY DIFFRACTIONc_scangle_it7.842.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.344 144 4.4 %
Rwork0.305 3013 -
obs--97 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.2126 / Rfactor Rfree: 0.2281
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.62
LS refinement shell
*PLUS
Rfactor obs: 0.305

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