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- PDB-3o1q: Native Crystal Structure of Helicobacter pylori Urease Accessory ... -

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Basic information

Entry
Database: PDB / ID: 3o1q
TitleNative Crystal Structure of Helicobacter pylori Urease Accessory Protein UreF
ComponentsUrease accessory protein ureF
KeywordsMETAL BINDING PROTEIN / urease maturation
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 / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsFong, Y.H. / Chen, Y.W. / Wong, K.B.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Assembly of Preactivation Complex for Urease Maturation in Helicobacter pylori: CRYSTAL STRUCTURE OF UreF-UreH PROTEIN COMPLEX.
Authors: Fong, Y.H. / Wong, H.C. / Chuck, C.P. / Chen, Y.W. / Sun, H. / Wong, K.B.
History
DepositionJul 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 2, 2011Group: Database references
Revision 1.3Dec 28, 2011Group: Database references
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)85,9563
Polymers85,9563
Non-polymers00
Water12,430690
1
A: Urease accessory protein ureF

A: Urease accessory protein ureF


Theoretical massNumber of molelcules
Total (without water)57,3042
Polymers57,3042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3270 Å2
ΔGint-19 kcal/mol
Surface area18340 Å2
MethodPISA
2
B: Urease accessory protein ureF
C: Urease accessory protein ureF


Theoretical massNumber of molelcules
Total (without water)57,3042
Polymers57,3042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-19 kcal/mol
Surface area18640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.328, 89.997, 66.950
Angle α, β, γ (deg.)90.00, 94.56, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-579-

HOH

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Components

#1: Protein Urease accessory protein ureF


Mass: 28651.834 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: ureF, HP_0069 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09065
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 690 / 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: 2.36 Å3/Da / Density % sol: 47.97 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM Bis-Tris pH 7.0 and 28% PEG MME 5000 , VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 10, 2010
RadiationMonochromator: rigkau varimax confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.85→50.95 Å / Num. all: 68238 / Num. obs: 68238 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.85-1.954.50.3343.998971100
5.85-50.954.70.108162229199.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIX(phenix.automr: 1.6.1_357model building
PHENIX(phenix.refine: 1.6.1_357)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIX1.6.1_357phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→40.225 Å / SU ML: 0.23 / σ(F): 1.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2083 2005 2.94 %RANDOM
Rwork0.1687 ---
all0.1699 68236 --
obs0.1699 68236 100 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.79 Å2 / ksol: 0.395 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.7844 Å20 Å2-2.5758 Å2
2---1.7557 Å2-0 Å2
3---2.54 Å2
Refinement stepCycle: LAST / Resolution: 1.85→40.225 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4936 0 0 690 5626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065065
X-RAY DIFFRACTIONf_angle_d0.9266855
X-RAY DIFFRACTIONf_dihedral_angle_d12.6931915
X-RAY DIFFRACTIONf_chiral_restr0.063803
X-RAY DIFFRACTIONf_plane_restr0.004873
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.89630.2181550.18284688X-RAY DIFFRACTION100
1.8963-1.94750.23161330.1824693X-RAY DIFFRACTION100
1.9475-2.00480.19841310.17664720X-RAY DIFFRACTION100
2.0048-2.06950.22951560.1654709X-RAY DIFFRACTION100
2.0695-2.14350.20011310.16054745X-RAY DIFFRACTION100
2.1435-2.22930.18671430.15724720X-RAY DIFFRACTION100
2.2293-2.33080.2211450.15754713X-RAY DIFFRACTION100
2.3308-2.45360.21151410.16354709X-RAY DIFFRACTION100
2.4536-2.60730.21211530.16614730X-RAY DIFFRACTION100
2.6073-2.80860.20191390.17764741X-RAY DIFFRACTION100
2.8086-3.09120.21741470.17254730X-RAY DIFFRACTION100
3.0912-3.53820.2091450.16174735X-RAY DIFFRACTION100
3.5382-4.45690.16131400.14044764X-RAY DIFFRACTION100
4.4569-40.23440.21181460.17594834X-RAY DIFFRACTION100

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