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- PDB-3cxn: Structure of the Urease Accessory Protein UreF from Helicobacter ... -

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Basic information

Entry
Database: PDB / ID: 3cxn
TitleStructure of the Urease Accessory Protein UreF from Helicobacter pylori
ComponentsUrease accessory protein ureF
KeywordsCHAPERONE / HELICAL / Nickel
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 / SAD / Resolution: 1.55 Å
AuthorsLam, R. / Johns, K. / Romanov, V. / Dong, A. / Wu-Brown, J. / Guthrie, J. / Dharamsi, A. / Thambipillai, D. / Mansoury, K. / Edwards, A.M. ...Lam, R. / Johns, K. / Romanov, V. / Dong, A. / Wu-Brown, J. / Guthrie, J. / Dharamsi, A. / Thambipillai, D. / Mansoury, K. / Edwards, A.M. / Pai, E.F. / Chirgadze, N.Y.
CitationJournal: Proteins / Year: 2010
Title: Crystal structure of a truncated urease accessory protein UreF from Helicobacter pylori.
Authors: Lam, R. / Romanov, V. / Johns, K. / Battaile, K.P. / Wu-Brown, J. / Guthrie, J.L. / Hausinger, R.P. / Pai, E.F. / Chirgadze, N.Y.
History
DepositionApr 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1094
Polymers94,0173
Non-polymers921
Water7,224401
1
B: Urease accessory protein ureF
hetero molecules

B: Urease accessory protein ureF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8624
Polymers62,6782
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3830 Å2
ΔGint-21 kcal/mol
Surface area17920 Å2
MethodPISA
2
A: Urease accessory protein ureF
C: Urease accessory protein ureF


Theoretical massNumber of molelcules
Total (without water)62,6782
Polymers62,6782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-19 kcal/mol
Surface area18430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.225, 89.418, 66.042
Angle α, β, γ (deg.)90.000, 94.030, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Urease accessory protein ureF


Mass: 31339.033 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: ureF / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: Q09065
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 21% PEG MME 2000, 0.1M BIS-TRIS, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 22, 2006 / Details: Si(111) double-crystal monochromator
RadiationMonochromator: Si(111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 112962 / % possible obs: 99.5 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.051 / Χ2: 1.517 / Net I/σ(I): 13.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.55-1.614.10.383112080.781199.1
1.61-1.674.20.276112210.815199.4
1.67-1.754.20.223112660.883199.5
1.75-1.844.20.169113100.918199.7
1.84-1.954.20.133113101.238199.8
1.95-2.14.20.08112681.372199.9
2.1-2.324.20.058113811.53199.9
2.32-2.654.20.049113381.7111100
2.65-3.344.20.041113772.2611100
3.34-504.10.036112833.692197.8

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Phasing

PhasingMethod: SAD
Phasing MAD set
IDR cullis acentricR cullis centricHighest resolution (Å)Lowest resolution (Å)Reflection acentricReflection centric
ISO_1001.5529.11099392729
ANO_10.76701.5529.11084340
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricReflection acentricReflection centric
ISO_16.75-29.1001094107
ISO_14.84-6.75002248142
ISO_13.97-4.84002897138
ISO_13.45-3.97003460146
ISO_13.09-3.45003908143
ISO_12.82-3.09004330141
ISO_12.61-2.82004673144
ISO_12.45-2.61005040142
ISO_12.31-2.45005392154
ISO_12.19-2.31005664138
ISO_12.09-2.19006035147
ISO_12-2.09006266135
ISO_11.92-2006539144
ISO_11.85-1.92006744132
ISO_11.79-1.85006996128
ISO_11.73-1.79007284139
ISO_11.68-1.73007539131
ISO_11.63-1.68007754128
ISO_11.59-1.63007907126
ISO_11.55-1.59008169124
ANO_16.75-29.10.366010030
ANO_14.84-6.750.395022320
ANO_13.97-4.840.502028580
ANO_13.45-3.970.533034350
ANO_13.09-3.450.543039030
ANO_12.82-3.090.544043260
ANO_12.61-2.820.576046680
ANO_12.45-2.610.628050370
ANO_12.31-2.450.669053830
ANO_12.19-2.310.798055850
ANO_12.09-2.190.787059990
ANO_12-2.090.846061710
ANO_11.92-20.885064670
ANO_11.85-1.920.919066210
ANO_11.79-1.850.946068900
ANO_11.73-1.790.967071690
ANO_11.68-1.730.977073990
ANO_11.63-1.680.985075960
ANO_11.59-1.630.991077420
ANO_11.55-1.590.997079500
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 112666
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.4-100740.666551
5.94-8.4590.8751303
4.85-5.9456.50.9191714
4.2-4.8555.20.9422013
3.76-4.256.70.9342269
3.43-3.7658.30.9412542
3.18-3.4358.10.9292703
2.97-3.1857.60.9162944
2.8-2.9757.30.9123103
2.66-2.859.20.9073295
2.53-2.6660.60.9083425
2.43-2.5360.20.913629
2.33-2.4361.40.9073783
2.25-2.3362.50.8993881
2.17-2.2563.50.9114089
2.1-2.1764.10.9134193
2.04-2.167.80.9184302
1.98-2.0467.30.9014463
1.93-1.98700.8684571
1.88-1.93720.8724660
1.83-1.88720.8344788
1.79-1.8373.40.8434891
1.75-1.7976.90.8545043
1.72-1.7575.70.865133
1.68-1.7277.80.8515223
1.65-1.6876.50.865366
1.62-1.6579.20.8485451
1.59-1.6279.50.8455482
1.55-1.5981.60.7767856

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DM5phasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT3.005data extraction
JDirectordata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.55→26.77 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.214 / WRfactor Rwork: 0.19 / SU B: 2.548 / SU ML: 0.046 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.211 5637 5 %RANDOM
Rwork0.187 ---
obs0.188 112662 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.178 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0.01 Å2
2---0.03 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.55→26.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4906 0 6 401 5313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225148
X-RAY DIFFRACTIONr_angle_refined_deg1.2361.986980
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3155664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.51726.104231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.328151000
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.2481511
X-RAY DIFFRACTIONr_chiral_restr0.0830.2813
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023777
X-RAY DIFFRACTIONr_nbd_refined0.2050.22622
X-RAY DIFFRACTIONr_nbtor_refined0.3050.23668
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2342
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.230
X-RAY DIFFRACTIONr_mcbond_it0.8681.53250
X-RAY DIFFRACTIONr_mcangle_it1.39325124
X-RAY DIFFRACTIONr_scbond_it2.32632102
X-RAY DIFFRACTIONr_scangle_it3.6424.51831
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.590.2354180.2057885839998.857
1.59-1.6340.2194080.1897615808099.295
1.634-1.6810.2194240.1867454792799.382
1.681-1.7320.2163940.197273770799.481
1.732-1.7890.2213660.1947054746099.464
1.789-1.8510.2443270.2026794717199.303
1.851-1.9210.2353710.2036487693998.833
1.921-1.9990.2253390.1896356671299.747
1.999-2.0870.2083180.1886075640299.859
2.087-2.1880.1912940.1765883617899.984
2.188-2.3060.2132780.1825527583599.486
2.306-2.4450.2072710.1835276556399.712
2.445-2.6120.2092690.1914895519599.403
2.612-2.8190.2252610.2014568485799.424
2.819-3.0850.2162380.24228448899.51
3.085-3.4430.211870.18238714058100
3.443-3.9650.181680.1623434360999.806
3.965-4.8290.181380.1672905306699.25
4.829-6.7210.2311160.2232276239999.708
6.721-26.7740.235520.21169142485.744
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.84490.9111-0.37151.7134-0.40850.3097-0.00870.0245-0.05450.1441-0.0288-0.1004-0.0148-0.00190.0375-0.0329-0.03790.0044-0.0098-0.007-0.030917.48118.7618.959
20.9843-0.09480.04880.260.08970.32570.07310.02790.0346-0.0019-0.0413-0.05870.02230.0153-0.0319-0.03940.01950.0074-0.01110.0102-0.015313.782-7.722-2.175
30.81310.2089-0.01480.54530.14330.94360.0757-0.01670.20890.11330.0316-0.079-0.0285-0.0167-0.1073-0.0079-0.0213-0.03-0.0702-0.01610.031328.16144.05723.447
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA27 - 23347 - 253
2X-RAY DIFFRACTION2BB25 - 23345 - 253
3X-RAY DIFFRACTION3CC25 - 23345 - 253

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