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- PDB-2bo3: Crystal Structure of HP0242, a Hypothetical Protein from Helicoba... -

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Basic information

Entry
Database: PDB / ID: 2bo3
TitleCrystal Structure of HP0242, a Hypothetical Protein from Helicobacter pylori
ComponentsHYPOTHETICAL PROTEIN HP0242
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / HELICOBACTER PYLORI / HYPOTHETICAL PROTEIN
Function / homologyHP0242-like domain / HP0242-like fold / Protein of unknown function DUF2018 / HP0242-like superfamily / Domain of unknown function (DUF2018) / Orthogonal Bundle / Mainly Alpha / metal ion binding / DUF2018 family protein
Function and homology information
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.27 Å
AuthorsSun, Y.-J. / Tsai, J.-Y. / Chen, B.-T.
CitationJournal: Proteins: Struct., Funct., Bioinf. / Year: 2006
Title: Crystal Structure of Hp0242, a Hypothetical Protein from Helicobacter Pylori with a Novel Fold
Authors: Tsai, J.-Y. / Chen H, B.-T. / Cheng, C. / Chen, H.Y. / Hsiao, N.W. / Liu, P.C. / Sun, Y.-J.
History
DepositionApr 7, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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: HYPOTHETICAL PROTEIN HP0242


Theoretical massNumber of molelcules
Total (without water)11,1021
Polymers11,1021
Non-polymers00
Water79344
1
A: HYPOTHETICAL PROTEIN HP0242

A: HYPOTHETICAL PROTEIN HP0242


Theoretical massNumber of molelcules
Total (without water)22,2032
Polymers22,2032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+7/41
MethodPQS
Unit cell
Length a, b, c (Å)44.300, 44.300, 119.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
DetailsREMARK: THE PROTEIN HAS A NOVEL FOLDING AND THE DIMERMIMICS A TIGHT FIGURE-OF-EIGHT KNOT STRUCTURE

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Components

#1: Protein HYPOTHETICAL PROTEIN HP0242


Mass: 11101.640 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Plasmid: PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: O25025
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growpH: 8.5 / Details: pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 0.9799
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 7, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9799 Å / Relative weight: 1
ReflectionResolution: 2.27→27.72 Å / Num. obs: 5957 / % possible obs: 93.6 % / Observed criterion σ(I): 2 / Redundancy: 11.9 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 37.2
Reflection shellResolution: 2.27→2.35 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 11.9 / % possible all: 92.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.27→27.72 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 311185.28 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.286 467 8.3 %RANDOM
Rwork0.254 ---
obs0.254 5624 93.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.9536 Å2 / ksol: 0.369059 e/Å3
Displacement parametersBiso mean: 48.4 Å2
Baniso -1Baniso -2Baniso -3
1-5.58 Å20 Å20 Å2
2--5.58 Å20 Å2
3----11.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.27→27.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms743 0 0 44 787
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.631.5
X-RAY DIFFRACTIONc_mcangle_it2.692
X-RAY DIFFRACTIONc_scbond_it2.412
X-RAY DIFFRACTIONc_scangle_it3.622.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.053 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.312 35 8.6 %
Rwork0.262 371 -
obs--38.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP

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