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- PDB-2wgl: Crystal structure of Helicobactor pylori UreF -

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Basic information

Entry
Database: PDB / ID: 2wgl
TitleCrystal structure of Helicobactor pylori UreF
ComponentsUREASE ACCESSORY PROTEIN UREF
KeywordsMETAL BINDING PROTEIN / CYTOPLASM / VIRULENCE / CHAPERONE / NICKEL INSERTION
Function / homology
Function and homology information


metabolic process / nickel cation binding / cytoplasm
Similarity search - Function
Urease accessory protein UreF / Urease accessory protein UreF / Urease accessory protein UreF / UreF domain superfamily / UreF / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Urease accessory protein UreF
Similarity search - Component
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2 Å
AuthorsFong, Y.H. / Chen, Y.W. / Wong, K.B.
CitationJournal: To be Published
Title: Crystal Structure of H. Pylori Uref
Authors: Fong, Y.H. / Chen, Y.W. / Wong, K.B.
History
DepositionApr 21, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 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 / 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 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UREASE ACCESSORY PROTEIN UREF
B: UREASE ACCESSORY PROTEIN UREF
C: UREASE ACCESSORY PROTEIN UREF


Theoretical massNumber of molelcules
Total (without water)87,3623
Polymers87,3623
Non-polymers00
Water9,476526
1
A: UREASE ACCESSORY PROTEIN UREF
C: UREASE ACCESSORY PROTEIN UREF


Theoretical massNumber of molelcules
Total (without water)58,2422
Polymers58,2422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-20.41 kcal/mol
Surface area18350 Å2
MethodPISA
2
B: UREASE ACCESSORY PROTEIN UREF

B: UREASE ACCESSORY PROTEIN UREF


Theoretical massNumber of molelcules
Total (without water)58,2422
Polymers58,2422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area3250 Å2
ΔGint-17.88 kcal/mol
Surface area18300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.163, 89.041, 65.994
Angle α, β, γ (deg.)90.00, 94.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein UREASE ACCESSORY PROTEIN UREF / UREF


Mass: 29120.783 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) HELICOBACTER PYLORI (bacteria) / Strain: 26695 / References: UniProt: Q09065
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.04 % / Description: NONE

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2→40.12 Å / Num. obs: 51513 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 10.3 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 14.3
Reflection shellResolution: 2→2.11 Å / Redundancy: 10 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.241 / % possible all: 93.9

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2→35.26 Å / SU ML: 0.08 / σ(F): 0.08 / Phase error: 22.04 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2324 2006 4.2 %
Rwork0.1903 --
obs0.1921 47763 90.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.741 Å2 / ksol: 0.361 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.7806 Å20 Å2-4.1434 Å2
2---3.6136 Å2-0 Å2
3---9.3942 Å2
Refinement stepCycle: LAST / Resolution: 2→35.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4968 0 0 526 5494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065067
X-RAY DIFFRACTIONf_angle_d0.9196846
X-RAY DIFFRACTIONf_dihedral_angle_d17.1951872
X-RAY DIFFRACTIONf_chiral_restr0.064798
X-RAY DIFFRACTIONf_plane_restr0.004870
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.28031190.24552550X-RAY DIFFRACTION72
2.05-2.10540.35111230.25852728X-RAY DIFFRACTION76
2.1054-2.16740.26241190.22192981X-RAY DIFFRACTION83
2.1674-2.23730.24721320.20343115X-RAY DIFFRACTION86
2.2373-2.31730.27911290.21183107X-RAY DIFFRACTION86
2.3173-2.410.21021590.17743317X-RAY DIFFRACTION92
2.41-2.51970.21031540.18033359X-RAY DIFFRACTION94
2.5197-2.65250.20311350.18573411X-RAY DIFFRACTION95
2.6525-2.81860.25321580.19753433X-RAY DIFFRACTION96
2.8186-3.03610.24431410.20343489X-RAY DIFFRACTION97
3.0361-3.34150.22761640.18813543X-RAY DIFFRACTION98
3.3415-3.82450.20381620.16643564X-RAY DIFFRACTION98
3.8245-4.81650.19021480.1553568X-RAY DIFFRACTION98
4.8165-35.26540.23211630.18063592X-RAY DIFFRACTION98

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