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- PDB-3k1h: Crystal structure of HP1076 from H.pylori -

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Basic information

Entry
Database: PDB / ID: 3k1h
TitleCrystal structure of HP1076 from H.pylori
ComponentsPutative uncharacterized protein
KeywordsCHAPERONE / FliS interacting protein / hypothetical protein
Function / homologyFlagellar FLiS export co-chaperone, HP1076 / Flagellar FLiS export co-chaperone, HP1076 / FLiS export co-chaperone, HP1076 superfamily / Flagellar FLiS export co-chaperone, HP1076 / Arylsulfatase, C-terminal domain / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.74 Å
AuthorsLam, W.W.L. / Ling, T.K.W. / Woo, E.J. / Au, S.W.N.
CitationJournal: Faseb J. / Year: 2010
Title: Molecular interaction of flagellar export chaperone FliS and cochaperone HP1076 in Helicobacter pylori
Authors: Lam, W.W.L. / Woo, E.J. / Kotaka, M. / Tam, W.K. / Leung, Y.C. / Ling, T.K.W. / Au, S.W.N.
History
DepositionSep 28, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2014Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)17,9901
Polymers17,9901
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.874, 87.202, 60.824
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-182-

HOH

21A-202-

HOH

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Components

#1: Protein Putative uncharacterized protein / HP1076


Mass: 17989.537 Da / Num. of mol.: 1 / Fragment: Residues 21-171
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: HP_1076 / Plasmid: pAc28m / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: O25709
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.29 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris, 27% PEG 3350, 0.2M Lithium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 0.97958 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 26, 2008
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 16258 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 45.8
Reflection shellResolution: 1.74→1.8 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.443 / Num. unique all: 1456 / % possible all: 90.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.74→26.06 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.698 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.105
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23305 819 5 %RANDOM
Rwork0.21006 ---
obs0.21118 15435 98.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.381 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2---0.06 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.74→26.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms906 0 0 82 988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022914
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1691.9961230
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6855114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.87227.544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67915183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.227152
X-RAY DIFFRACTIONr_chiral_restr0.0810.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02665
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6821.5572
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3422920
X-RAY DIFFRACTIONr_scbond_it2.3993342
X-RAY DIFFRACTIONr_scangle_it4.1794.5310
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.737→1.782 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 55 -
Rwork0.341 997 -
obs--87.52 %
Refinement TLS params.Method: refined / Origin x: 11.568 Å / Origin y: 14.602 Å / Origin z: -18.096 Å
111213212223313233
T0.0435 Å2-0.0186 Å20.0037 Å2-0.0124 Å2-0.0052 Å2--0.0116 Å2
L0.9969 °21.2621 °21.3246 °2-1.812 °21.6023 °2--1.7873 °2
S-0.0604 Å °0.0808 Å °-0.0208 Å °-0.014 Å °0.0791 Å °-0.0436 Å °-0.0965 Å °0.1129 Å °-0.0186 Å °

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