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- PDB-4u12: Crystal structure of protein HP0242 from Helicobacter pylori at 1... -

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Basic information

Entry
Database: PDB / ID: 4u12
TitleCrystal structure of protein HP0242 from Helicobacter pylori at 1.94 A resolution: a knotted homodimer
ComponentsUncharacterized protein HP0242
KeywordsStructural Genomics / Unknown Function / PSI-2 / Midwest Center for Structural Genomics / MCSG / Knotted homodimer / HELICOBACTER PYLORI / Protein Structure Initiative
Function / homologyHP0242-like domain / HP0242-like fold / Protein of unknown function DUF2018 / HP0242-like superfamily / Domain of unknown function (DUF2018) / Orthogonal Bundle / metal ion binding / Mainly Alpha / DUF2018 family protein
Function and homology information
Biological speciesHelicobacter pylori 26695 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.94 Å
AuthorsGrabowski, M. / Shabalin, I.G. / Chruszcz, M. / Skarina, T. / Onopriyenko, O. / Guthrie, J. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM053163 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54-GM094585-04 United States
CitationJournal: to be published
Title: Crystal structure of protein HP0242 from Helicobacter pylori at 1.94 A resolution: a knotted homodimer
Authors: Grabowski, M. / Shabalin, I.G. / Chruszcz, M. / Skarina, T. / Onopriyenko, O. / Guthrie, J. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W.
History
DepositionJul 14, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionJul 23, 2014ID: 2OUF
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Structure summary
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Apr 13, 2022Group: Database references / Refinement description / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / refine_hist
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein HP0242


Theoretical massNumber of molelcules
Total (without water)11,1951
Polymers11,1951
Non-polymers00
Water1,24369
1
A: Uncharacterized protein HP0242

A: Uncharacterized protein HP0242


Theoretical massNumber of molelcules
Total (without water)22,3912
Polymers22,3912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/41
Buried area4070 Å2
ΔGint-37 kcal/mol
Surface area8850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.944, 44.944, 117.883
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Detailsbiological unit is the same as asym.

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Components

#1: Protein Uncharacterized protein HP0242


Mass: 11195.431 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: forms a knotted homodimer / Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Gene: C694_01225, HP_0242 / Plasmid: p11 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Codonplus(de3) Rp / References: UniProt: O25025
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.68 Å3/Da / Density % sol: 54.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 30% v/v Pentaerythritol Ethoxylate (15/4 EO/OH), 0.05M Ammonium Sulfate, 0.05M Bis-Tris, pH 6.5,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97904 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jun 9, 2006 / Details: Mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 9566 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Redundancy: 16 % / Biso Wilson estimate: 36.3 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Χ2: 0.824 / Net I/av σ(I): 46.12 / Net I/σ(I): 8.7 / Num. measured all: 153490
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.94-1.9716.70.9374650.512100
1.97-2.01170.7284590.481100
2.01-2.0516.70.574720.483100
2.05-2.0916.80.4914490.469100
2.09-2.1416.70.3424820.461100
2.14-2.1816.60.3224510.474100
2.18-2.2416.80.2594730.496100
2.24-2.316.40.2234530.504100
2.3-2.3716.60.1924760.514100
2.37-2.4416.40.1614710.564100
2.44-2.5316.50.124650.614100
2.53-2.6316.30.1084860.659100
2.63-2.7516.30.0854660.768100
2.75-2.916.10.0794720.852100
2.9-3.08160.0634790.986100
3.08-3.3215.70.0524891.105100
3.32-3.6515.60.0454801.13399.8
3.65-4.1814.90.0425071.202100
4.18-5.2613.40.045121.485100
5.26-5014.10.0425592.83497

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
SCALEPACKdata scaling
HKL-3000phasing
SHELXDEphasing
DMphasing
RESOLVEphasing
ARPmodel building
Cootmodel building
PDB_EXTRACT3.14data extraction
REFMAC5.8.0049refinement
RefinementMethod to determine structure: SAD / Resolution: 1.94→44.94 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.2502 / WRfactor Rwork: 0.2234 / FOM work R set: 0.8101 / SU B: 7.995 / SU ML: 0.113 / SU R Cruickshank DPI: 0.1455 / SU Rfree: 0.1388 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2533 457 4.8 %RANDOM
Rwork0.2208 9069 --
obs0.2224 9526 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 158.09 Å2 / Biso mean: 65.103 Å2 / Biso min: 26.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å2-0 Å2
2--0.17 Å20 Å2
3----0.35 Å2
Refinement stepCycle: final / Resolution: 1.94→44.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms626 0 0 69 695
Biso mean---61.72 -
Num. residues----80
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.019637
X-RAY DIFFRACTIONr_bond_other_d0.0030.02619
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.991859
X-RAY DIFFRACTIONr_angle_other_deg0.80431427
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.217581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.83826.55229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.7515121
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.492152
X-RAY DIFFRACTIONr_chiral_restr0.0820.2102
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02711
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02129
X-RAY DIFFRACTIONr_mcbond_it1.6012.422321
X-RAY DIFFRACTIONr_mcbond_other1.5852.414320
X-RAY DIFFRACTIONr_mcangle_it2.2613.607400
LS refinement shellResolution: 1.942→1.993 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 31 -
Rwork0.273 648 -
all-679 -
obs--99.41 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
113.7748-2.82652.85875.83171.496815.89370.4701-0.6115-0.3289-0.37430.2104-0.05270.949-0.2702-0.68050.1209-0.0447-0.0630.11660.080.084425.46817.47422.307
29.44225.7832-1.87848.4114-4.12787.15910.1779-0.37180.0960.08950.03120.4448-0.7159-0.3757-0.20920.1270.03550.01410.11780.00440.10122.68130.98116.243
315.7553-18.30321.011938.6768-18.593617.85290.8527-1.28950.37780.3674-1.6469-1.0445-1.59543.88310.79420.5403-1.0006-0.16172.55460.39210.181641.8137.66610.179
441.3704-9.0434-10.58297.2895-5.315417.74610.35310.2377-1.06750.5476-1.065-0.5849-0.22720.95910.71190.2966-0.1182-0.190.81360.18050.341845.3724.01620.685
527.433-2.10635.19961.9897-4.18049.42650.899-1.4138-0.08170.0877-0.1940.2253-0.31180.1009-0.70510.2107-0.00620.04930.34740.03590.158627.81226.40625.536
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 23
2X-RAY DIFFRACTION2A24 - 47
3X-RAY DIFFRACTION3A48 - 62
4X-RAY DIFFRACTION4A63 - 75
5X-RAY DIFFRACTION5A76 - 92

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