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- PDB-3na7: 2.2 Angstrom Structure of the HP0958 Protein from Helicobacter py... -

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Basic information

Entry
Database: PDB / ID: 3na7
Title2.2 Angstrom Structure of the HP0958 Protein from Helicobacter pylori CCUG 17874
ComponentsHP0958
KeywordsGene Regulation / Chaperone / flagellar biogenesis / flagellum export / C4 Zn-ribbon / Coiled-coil / post-transcriptional
Function / homologyHelix Hairpins - #1490 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsCaly, D.L. / O'Toole, P.W. / Moore, S.A.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: The 2.2-A Structure of the HP0958 Protein from Helicobacter pylori Reveals a Kinked Anti-Parallel Coiled-Coil Hairpin Domain and a Highly Conserved Zn-Ribbon Domain
Authors: Caly, D.L. / O'Toole, P.W. / Moore, S.A.
History
DepositionJun 1, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 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_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: HP0958
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1274
Polymers29,7991
Non-polymers3283
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)172.720, 37.951, 66.056
Angle α, β, γ (deg.)90.00, 110.66, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein HP0958


Mass: 29799.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: CCUG 17874 / Gene: HP0958 / Plasmid details: Glutathione S-Transferase fusion vector / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNO SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN CURRENTLY EXISTS IN UNIPROT. THE RESIDUES, 72, 120, ...NO SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN CURRENTLY EXISTS IN UNIPROT. THE RESIDUES, 72, 120, 139, 140, 141, 166, 238, AND 239 ARE STRAIN SPECIFIC VARIATIONS RELATIVE TO STRAIN 26695.

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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: 3.4 Å3/Da / Density % sol: 63.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18% PEG 3350, 0.1M HEPES pH 7.5, 0.2M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.984 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 24, 2008 / Details: Mirrors
RadiationMonochromator: Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 20734 / Num. obs: 19056 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 5 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 33.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1327 / Rsym value: 0.22 / % possible all: 65.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.907 / SU B: 13.592 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29378 981 5.2 %RANDOM
Rwork0.24844 ---
obs0.25067 18062 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 61.009 Å2
Baniso -1Baniso -2Baniso -3
1--1.58 Å20 Å20.77 Å2
2--5.64 Å20 Å2
3----3.52 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1928 0 17 49 1994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221957
X-RAY DIFFRACTIONr_angle_refined_deg1.3162.0032613
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5395236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.91526.27794
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.02115438
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6781512
X-RAY DIFFRACTIONr_chiral_restr0.0950.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021383
X-RAY DIFFRACTIONr_mcbond_it1.3381.51181
X-RAY DIFFRACTIONr_mcangle_it2.4521909
X-RAY DIFFRACTIONr_scbond_it3.5963776
X-RAY DIFFRACTIONr_scangle_it5.6023.5704
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.322 41
Rwork0.304 893
obs-934
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)
12.91452.1412-4.2212.2036-3.31986.3771-0.02020.12440.03230.09950.26260.1274-0.1977-0.3438-0.24240.20440.11090.06610.11420.1060.20614.24272.939267.2749
27.538-3.3041-6.93571.67623.00277.2607-0.08890.0123-0.0951-0.02540.046-0.0040.09080.18690.04280.0748-0.0137-0.04160.0589-0.02440.071945.6192-0.563529.1996
30.41120.98941.13562.51843.17575.6335-0.04210.02880.1752-0.1264-0.10110.4083-0.0668-0.58910.14320.13590.0114-0.03770.28170.11770.2102-8.7764-15.190466.1061
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 28
2X-RAY DIFFRACTION1A144 - 167
3X-RAY DIFFRACTION2A29 - 83
4X-RAY DIFFRACTION2A91 - 143
5X-RAY DIFFRACTION3A170 - 235

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