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- PDB-2evv: Crystal Structure of the PEBP-like Protein of Unknown Function HP... -

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Basic information

Entry
Database: PDB / ID: 2evv
TitleCrystal Structure of the PEBP-like Protein of Unknown Function HP0218 from Helicobacter pylori
Componentshypothetical protein HP0218
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta structure / dimer / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


outer membrane-bounded periplasmic space
Similarity search - Function
YbhB/YbcL / Phosphatidylethanolamine-binding Protein / PEBP-like / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / PEBP-like superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
YbhB/YbcL family Raf kinase inhibitor-like protein
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.59 Å
AuthorsKim, Y. / Xu, X. / Hong, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of the Hypothetical Protein HP0218 from Helicobacter pylori
Authors: Kim, Y. / Xu, X. / Hong, H. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionNov 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 20, 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

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein HP0218
B: hypothetical protein HP0218
C: hypothetical protein HP0218
D: hypothetical protein HP0218
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6929
Polymers95,2284
Non-polymers4645
Water4,810267
1
A: hypothetical protein HP0218
B: hypothetical protein HP0218
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8945
Polymers47,6142
Non-polymers2803
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-30 kcal/mol
Surface area16650 Å2
MethodPISA
2
C: hypothetical protein HP0218
D: hypothetical protein HP0218
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7984
Polymers47,6142
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-18 kcal/mol
Surface area16400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.312, 102.266, 143.047
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
hypothetical protein HP0218


Mass: 23806.879 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: HP0218 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: O25006
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 3.93 Å3/Da / Density % sol: 68.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M Bis-Tris PH6.0, 0.2M Ammonium Sulphate, 20%PEG4K, 2% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97922 Å
DetectorType: SBC-3 / Detector: CCD / Date: Apr 3, 2005 / Details: mirrors
RadiationMonochromator: double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 2.59→45.75 Å / Num. all: 48287 / Num. obs: 47122 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Rmerge(I) obs: 0.191 / Net I/σ(I): 4.9
Reflection shellResolution: 2.59→2.68 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.798 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3786 / % possible all: 79.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0000refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXphasing
SOLVEphasing
RESOLVEphasing
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 2.59→45.75 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.871 / SU B: 16.496 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.366 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CNS 1.1 was also used in refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.26248 4630 10.1 %RANDOM
Rwork0.2191 ---
all0.2235 41287 --
obs0.2235 41287 97.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.218 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2---1.79 Å20 Å2
3---1.57 Å2
Refinement stepCycle: LAST / Resolution: 2.59→45.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5752 0 29 267 6048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226118
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.9548283
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.585758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36424.81289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.527151083
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7131525
X-RAY DIFFRACTIONr_chiral_restr0.0950.2866
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024709
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.23074
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2363
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2660.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8281.53824
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.22726022
X-RAY DIFFRACTIONr_scbond_it1.84232605
X-RAY DIFFRACTIONr_scangle_it2.8484.52261
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.592→2.66 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.386 304
Rwork0.323 2909
obs-2909

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