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- PDB-2i9i: Crystal Structure of Helicobacter pylori protein HP0492 -

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Basic information

Entry
Database: PDB / ID: 2i9i
TitleCrystal Structure of Helicobacter pylori protein HP0492
ComponentsHypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyPutative neuraminyllactose-binding hemagglutinin homolog like domain / Neuraminyllactose-binding hemagglutinin / Neuraminyllactose-binding hemagglutinin superfamily / Neuraminyllactose-binding hemagglutinin precursor (NLBH) / Double Stranded RNA Binding Domain / cell outer membrane / 2-Layer Sandwich / Alpha Beta / Neuraminyllactose-binding hemagglutinin
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsBonanno, J.B. / Dickey, M. / Bain, K.T. / Mckenzie, C. / Ozyurt, S. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of Helicobacter pylori hypothetical protein O25234
Authors: Bonanno, J.B. / Dickey, M. / Bain, K.T. / Mckenzie, C. / Ozyurt, S. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionSep 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.6Feb 21, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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: Hypothetical protein


Theoretical massNumber of molelcules
Total (without water)29,5261
Polymers29,5261
Non-polymers00
Water2,810156
1
A: Hypothetical protein

A: Hypothetical protein


Theoretical massNumber of molelcules
Total (without water)59,0532
Polymers59,0532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area3720 Å2
ΔGint-11 kcal/mol
Surface area20680 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.544, 82.803, 126.236
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Detailspossible dimer

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Components

#1: Protein Hypothetical protein /


Mass: 29526.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Plasmid: modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O25234
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.32 Å3/Da / Density % sol: 47.08 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 30% PEG 8K, 200mM Na Acetate pH 4.6, 100mM Na Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 17, 2006
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 25929 / Num. obs: 25929 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.1 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.225 / Rsym value: 0.208 / Net I/σ(I): 9.6
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.895 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3733 / Rsym value: 0.831 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345CCDdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.038 / SU ML: 0.095 / Isotropic thermal model: Iso11_refmac5.logtropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.128 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24926 1314 5.1 %RANDOM
Rwork0.20364 ---
all0.2059 24549 --
obs0.2059 24500 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.075 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20 Å2
2--1.75 Å20 Å2
3----2.37 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 0 156 1965
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221851
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.9432512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1085230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.28524.89192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5715336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.696159
X-RAY DIFFRACTIONr_chiral_restr0.1250.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021403
X-RAY DIFFRACTIONr_nbd_refined0.2070.2740
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21255
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2118
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.220
X-RAY DIFFRACTIONr_mcbond_it1.1641.51153
X-RAY DIFFRACTIONr_mcangle_it1.79321822
X-RAY DIFFRACTIONr_scbond_it3.1983790
X-RAY DIFFRACTIONr_scangle_it5.0044.5685
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 102 -
Rwork0.321 1766 -
obs--100 %

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