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- PDB-5j4f: Crystal structure of the N-terminally His6-tagged HP0902, an unch... -

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Basic information

Entry
Database: PDB / ID: 5j4f
TitleCrystal structure of the N-terminally His6-tagged HP0902, an uncharacterized protein from Helicobacter pylori 26695
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / HP0902 / Helicobacter pylori / secretory protein / Cupin family / Uncharacterized protein
Function / homologyCupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / Cupin type-2 domain-containing protein
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSim, D.-W. / Lee, W.-C. / Kim, H.Y. / Kim, J.-H. / Won, H.-S.
CitationJournal: FEBS Lett. / Year: 2016
Title: Structural identification of the lipopolysaccharide-binding capability of a cupin-family protein from Helicobacter pylori
Authors: Sim, D.W. / Kim, J.H. / Kim, H.Y. / Jang, J.H. / Lee, W.C. / Kim, E.H. / Park, P.J. / Lee, K.H. / Won, H.S.
History
DepositionApr 1, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)26,4392
Polymers26,4392
Non-polymers00
Water3,171176
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-3 kcal/mol
Surface area9140 Å2
Unit cell
Length a, b, c (Å)33.512, 78.643, 41.404
Angle α, β, γ (deg.)90.00, 112.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein


Mass: 13219.380 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Strain: ATCC 700392 / 26695 / Gene: HP_0902 / Production host: Escherichia coli (E. coli) / References: UniProt: O25562
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 1.91 Å3/Da / Density % sol: 35.61 % / Description: short needle
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 3350, sodium chloride, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 12, 2010
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.4→71 Å / Num. obs: 38998 / % possible obs: 99.8 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 15.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata processing
SCALAdata scaling
MOLREPphasing
SHELXDEmodel building
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2q30

2q30


Resolution: 1.4→19.85 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.102 / SU ML: 0.044 / Cross valid method: FREE R-VALUE / ESU R: 0.061 / ESU R Free: 0.063 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20779 1952 5 %RANDOM
Rwork0.18076 ---
obs0.18211 37000 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 19.028 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.07 Å2
2---0.08 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.4→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 0 176 1692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0221536
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3671.9862061
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4095193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.08525.48462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16415312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.972156
X-RAY DIFFRACTIONr_chiral_restr0.1640.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211092
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_it1.511.5968
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.75821564
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.5673568
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.8534.5497
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 163 -
Rwork0.297 2671 -
obs--99.61 %

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