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- PDB-2uvp: Crystal structure of HobA (HP1230)from Helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 2uvp
TitleCrystal structure of HobA (HP1230)from Helicobacter pylori
Components(HOBA) x 2
KeywordsUNKNOWN FUNCTION / HYPOTHETICAL PROTEIN / DNAA / SIS FOLD / DNA REPLICATION
Function / homology
Function and homology information


metal ion binding / identical protein binding
Similarity search - Function
DNA replication regulator HobA / DNA replication regulator, HobA / DNA replication regulator HobA superfamily / DNA replication regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / DNA replication regulator protein HobA
Similarity search - Component
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsTerradot, L. / Natrajan, G. / Thompson, A.C. / Hall, D.R.
CitationJournal: Mol. Microbiol. / Year: 2007
Title: Structural similarity between the DnaA-binding proteins HobA (HP1230) from Helicobacter pylori and DiaA from Escherichia coli.
Authors: Natrajan, G. / Hall, D.R. / Thompson, A.C. / Gutsche, I. / Terradot, L.
History
DepositionMar 13, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Jun 13, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / diffrn ...citation / diffrn / diffrn_detector / diffrn_radiation / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _diffrn.ambient_temp / _diffrn_detector.pdbx_collection_date / _diffrn_radiation.monochromator / _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: HOBA
B: HOBA
C: HOBA
D: HOBA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,07914
Polymers86,5174
Non-polymers56210
Water15,349852
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13710 Å2
ΔGint-133.8 kcal/mol
Surface area39030 Å2
MethodPQS
Unit cell
Length a, b, c (Å)112.232, 112.232, 61.929
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 4 / Auth seq-ID: 90 - 97 / Label seq-ID: 96 - 103

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein HOBA


Mass: 21639.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: FOUR CALCIUM ATOMS IN THE STRUCTURE / Source: (gene. exp.) HELICOBACTER PYLORI (bacteria)
Description: BACTERIA THAT IS FOUND IN THE GUT. AFFECTS AROUND A THIRD OF THE WORLD'S POPULATION AND IS A LEADING CAUSE OF ULCERS AND GASTRITIS
Plasmid: PPHP1230 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star pLysS / References: UniProt: O25828
#2: Protein HOBA


Mass: 21625.857 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: FOUR CALCIUM ATOMS IN THE STRUCTURE / Source: (gene. exp.) HELICOBACTER PYLORI (bacteria)
Description: BACTERIA THAT IS FOUND IN THE GUT. AFFECTS AROUND A THIRD OF THE WORLD'S POPULATION AND IS A LEADING CAUSE OF ULCERS AND GASTRITIS
Plasmid: PPHP1230 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star pLysS / References: UniProt: O25828

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Non-polymers , 4 types, 862 molecules

#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 852 / 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: 2.78 Å3/Da / Density % sol: 55.78 % / Description: NATIVE DATA SET
Crystal growpH: 5.5
Details: 100 MM MES PH 5.6, 300 MM CA ACETATE, 14-20% PEG 3350.

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11731
21731
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF ID14-310.934
SYNCHROTRONESRF ID23-121.77
Detector
TypeIDDetectorDateDetails
MARRESEARCH1CCDDec 1, 2005MIRRORS
MARRESEARCH2CCDDec 1, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GE 220 DIAMOND 111SINGLE WAVELENGTHMx-ray1
2GE 220 DIAMOND 111SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9341
21.771
ReflectionResolution: 1.7→41.59 Å / Num. obs: 95964 / % possible obs: 100 % / Redundancy: 4.6 % / Biso Wilson estimate: 19.43 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.8
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 1.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.3.0011refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.7→97.13 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.966 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.214 4808 5 %RANDOM
Rwork0.18 ---
obs0.182 91127 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: 21.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20.16 Å20 Å2
2--0.32 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.7→97.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5959 0 29 852 6840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226223
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.9648426
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1725738
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.04524.983293
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.914151132
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5051517
X-RAY DIFFRACTIONr_chiral_restr0.1460.2927
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024643
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.23373
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.24312
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2707
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.283
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.236
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0151.53783
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6725926
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.26832831
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.524.52500
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 47 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.990.5
2Bmedium positional0.780.01
3Cmedium positional1.320
4Dmedium positional0.890
1Amedium thermal1.232
2Bmedium thermal1.030.04
3Cmedium thermal1.340
4Dmedium thermal1.170
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.32 341
Rwork0.26 6736

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