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- PDB-2gts: Structure of Protein of Unknown Function HP0062 from Helicobacter... -

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Basic information

Entry
Database: PDB / ID: 2gts
TitleStructure of Protein of Unknown Function HP0062 from Helicobacter pylori
Componentshypothetical protein HP0062
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / MCSG / hypothetical protein / Helicobacter pylori / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homologyHP0062-like domain superfamily / HP0062-like domain / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / : / Type VII secretion protein
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsBinkowski, T.A. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Hypothetical protein HP0062 from Helicobacter pylori
Authors: Binkowski, T.A. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionApr 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 30, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein HP0062


Theoretical massNumber of molelcules
Total (without water)10,6261
Polymers10,6261
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: hypothetical protein HP0062

A: hypothetical protein HP0062


Theoretical massNumber of molelcules
Total (without water)21,2532
Polymers21,2532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3450 Å2
ΔGint-28 kcal/mol
Surface area9080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)43.494, 43.494, 97.639
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein hypothetical protein HP0062


Mass: 10626.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: GeneID:899000, HP0062 / Production host: Escherichia coli (E. coli) / References: GenBank: 15644692, UniProt: O24902*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.51 Å3/Da / Density % sol: 50.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Na Citrate 1.4M, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97945 Å
DetectorType: SBC-2 / Detector: CCD / Date: Feb 14, 2005
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 6359 / Num. obs: 6035 / % possible obs: 94.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.1→2.155 Å / % possible all: 64.02

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.1→29.83 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.907 / SU B: 15.219 / SU ML: 0.189 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.225 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29686 294 4.6 %RANDOM
Rwork0.22189 ---
all0.2278 6359 --
obs0.2254 6035 94.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.589 Å2
Baniso -1Baniso -2Baniso -3
1-2.02 Å21.01 Å20 Å2
2--2.02 Å20 Å2
3----3.03 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms663 0 0 30 693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.021675
X-RAY DIFFRACTIONr_angle_refined_deg2.0351.919905
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.601576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.0872445
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.6415128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.931158
X-RAY DIFFRACTIONr_chiral_restr0.150.293
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02528
X-RAY DIFFRACTIONr_nbd_refined0.2450.2251
X-RAY DIFFRACTIONr_nbtor_refined0.3190.2462
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3270.226
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3890.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4120.213
X-RAY DIFFRACTIONr_mcbond_it1.1351.5399
X-RAY DIFFRACTIONr_mcangle_it1.8892615
X-RAY DIFFRACTIONr_scbond_it3.1623315
X-RAY DIFFRACTIONr_scangle_it5.0324.5290
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.666 19 -
Rwork0.285 287 -
obs--64.02 %
Refinement TLS params.Method: refined / Origin x: 5.6136 Å / Origin y: 19.4821 Å / Origin z: 2.1015 Å
111213212223313233
T-0.2934 Å20.0788 Å2-0.0115 Å2--0.3842 Å2-0.0349 Å2---0.3986 Å2
L5.461 °2-0.9036 °24.7142 °2-2.6332 °2-1.1255 °2--8.6192 °2
S-0.62 Å °-0.1145 Å °0.5335 Å °0.431 Å °0.2757 Å °-0.1615 Å °-0.662 Å °-0.7355 Å °0.3442 Å °

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