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- PDB-2atz: Crystal structure of protein HP0184 from Helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 2atz
TitleCrystal structure of protein HP0184 from Helicobacter pylori
ComponentsH. pylori predicted coding region HP0184
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Helicobacter pylori / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyHP0184-like / Domain of unknown function DUF1882 / HP0184-like superfamily / Domain of unknown function (DUF1882) / DNA primase, PRIM domain / Alpha-Beta Complex / Alpha Beta / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / DUF1882 domain-containing protein
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsChang, C. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of protein HP0184 from Helicobacter pylori
Authors: Chang, C. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionAug 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Nov 13, 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

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Assembly

Deposited unit
A: H. pylori predicted coding region HP0184
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0493
Polymers21,4801
Non-polymers5692
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.093, 77.093, 118.187
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein H. pylori predicted coding region HP0184


Mass: 21480.002 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Production host: Escherichia coli (E. coli) / References: UniProt: O24984
#2: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.4 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: Tris, CL, PEG3350, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 19, 2005
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 14694 / Num. obs: 14653 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 19.5 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 63.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 4.95 / Num. unique all: 1385 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.629 / SU ML: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25567 734 5 %RANDOM
Rwork0.19789 ---
all0.20069 14606 --
obs0.20069 14606 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.648 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0.12 Å20 Å2
2---0.25 Å20 Å2
3---0.37 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1461 0 35 100 1596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221535
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9061.9792070
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5525175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.18123.46775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.72115279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5941510
X-RAY DIFFRACTIONr_chiral_restr0.1330.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021146
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.2662
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.2992
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.296
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3280.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7732902
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.5831406
X-RAY DIFFRACTIONr_scbond_it2.162736
X-RAY DIFFRACTIONr_scangle_it3.1633664
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 56 -
Rwork0.229 958 -
obs--96.57 %
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)
13.5325-1.435-1.109811.79092.61016.20830.41280.7837-0.3555-0.8189-0.72710.29920.0399-0.470.3143-0.24560.065-0.02940.0662-0.1012-0.2802-8.48130.807-5.973
213.76330.9870.1647.1662.425518.85910.43631.1652-1.2925-0.3549-0.6630.23371.5846-0.360.22670.04650.0093-0.052-0.0013-0.26090.0177-3.21916.436-9.392
34.0702-1.8706-1.31523.0193.54066.475-0.1198-0.2155-0.02580.26080.469-0.33250.39290.7507-0.3492-0.2250.0562-0.0159-0.1711-0.0461-0.27933.76128.8067.533
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 443 - 44
2X-RAY DIFFRACTION2AA45 - 5945 - 59
3X-RAY DIFFRACTION3AA60 - 17860 - 178

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