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- PDB-2wp0: Crystal structure of a HobA-DnaA (domain I-II) complex from Helic... -

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Basic information

Entry
Database: PDB / ID: 2wp0
TitleCrystal structure of a HobA-DnaA (domain I-II) complex from Helicobacter pylori.
Components
  • CHROMOSOMAL REPLICATION INITIATOR PROTEIN DNAA
  • HOBA
KeywordsDNA BINDING PROTEIN / NUCLEOTIDE-BINDING / DNA REPLICATION INITIATION / DIAA / HOBA / DNAA / ATP-BINDING
Function / homology
Function and homology information


DNA replication origin binding / regulation of DNA replication / DNA replication initiation / DNA replication / ATP binding / identical protein binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
DNA replication regulator HobA / DNA replication regulator, HobA / DNA replication regulator HobA superfamily / DNA replication regulator / DnaA, N-terminal domain / DnaA, N-terminal domain superfamily / Chromosomal replication control, initiator DnaA / Chromosomal replication initiator, DnaA C-terminal / Chromosomal replication control, initiator DnaA, conserved site / Bacterial dnaA protein helix-turn-helix ...DNA replication regulator HobA / DNA replication regulator, HobA / DNA replication regulator HobA superfamily / DNA replication regulator / DnaA, N-terminal domain / DnaA, N-terminal domain superfamily / Chromosomal replication control, initiator DnaA / Chromosomal replication initiator, DnaA C-terminal / Chromosomal replication control, initiator DnaA, conserved site / Bacterial dnaA protein helix-turn-helix / DnaA protein signature. / Bacterial dnaA protein helix-turn-helix domain / Chromosomal replication control, initiator DnaA-like / Chromosomal replication initiator protein DnaA / Bacterial dnaA protein / Trp repressor/replication initiator / GMP Synthetase; Chain A, domain 3 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / DNA replication regulator family protein / Chromosomal replication initiator protein DnaA
Similarity search - Component
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsNatrajan, G. / Noirot-Gros, M.-F. / Zawilak-Pawlik, A. / Kapp, U. / Terradot, L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: The Structure of a Dnaa/Hoba Complex from Helicobacter Pylori Provides Insight Into Regulation of DNA Replication in Bacteria.
Authors: Natrajan, G. / Noirot-Gros, M.F. / Zawilak-Pawlik, A. / Kapp, U. / Terradot, L.
History
DepositionJul 31, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.4Dec 20, 2023Group: 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_initial_refinement_model / struct_conn
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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HOBA
B: HOBA
C: CHROMOSOMAL REPLICATION INITIATOR PROTEIN DNAA
D: CHROMOSOMAL REPLICATION INITIATOR PROTEIN DNAA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,05224
Polymers67,3434
Non-polymers70920
Water1,928107
1
A: HOBA
B: HOBA
C: CHROMOSOMAL REPLICATION INITIATOR PROTEIN DNAA
D: CHROMOSOMAL REPLICATION INITIATOR PROTEIN DNAA
hetero molecules

A: HOBA
B: HOBA
C: CHROMOSOMAL REPLICATION INITIATOR PROTEIN DNAA
D: CHROMOSOMAL REPLICATION INITIATOR PROTEIN DNAA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,10448
Polymers134,6878
Non-polymers1,41840
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area22070 Å2
ΔGint-381.17 kcal/mol
Surface area48030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.560, 55.500, 96.830
Angle α, β, γ (deg.)90.00, 97.55, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 1:180 )
211CHAIN B AND (RESSEQ 1:180 )
112CHAIN C AND (RESSEQ 10:74 OR RESSEQ 80:91 )
212CHAIN D AND (RESSEQ 10:74 OR RESSEQ 80:91 )

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein HOBA


Mass: 21039.197 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: HOBA PROTEIN (HP 1230) / Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O25828
#2: Protein CHROMOSOMAL REPLICATION INITIATOR PROTEIN DNAA


Mass: 12632.481 Da / Num. of mol.: 2 / Fragment: DOMAIN I-II, RESIDUES 1-120
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL FRAGMENT OF DNAA / Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O26057

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Non-polymers , 5 types, 127 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE ACCESSION NUMBER IS FOR THE FULL LENGTH PROTEIN

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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: 2.63 Å3/Da / Density % sol: 53.3 %
Description: A COMBINATION OF 2UVP FOR HOBA AND A HOMOLGY MODEL FOR DNAA I-II WAS USED FOR MOLECULAR REPLACEMENT.
Crystal growpH: 8
Details: 100 MM TRIS-HCL PH 8.0, 200 MM K-ACETATE, 19-22% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.91
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 17, 2008 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.67→50.77 Å / Num. obs: 17498 / % possible obs: 93.4 % / Observed criterion σ(I): 1.1 / Redundancy: 2.6 % / Biso Wilson estimate: 39.3 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.8
Reflection shellResolution: 2.67→2.81 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.7 / % possible all: 94.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UVP

2uvp


Resolution: 2.67→50.756 Å / SU ML: 0.41 / σ(F): 1.34 / Phase error: 27.95 / Stereochemistry target values: ML / Details: RESIDUE 75 MISSING FROM CHAIN C.
RfactorNum. reflection% reflection
Rfree0.2663 897 5.17 %
Rwork0.2262 --
obs0.2283 17357 90.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.375 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.9313 Å2-0 Å20.9037 Å2
2---1.8336 Å2-0 Å2
3---9.8006 Å2
Refinement stepCycle: LAST / Resolution: 2.67→50.756 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4339 0 33 107 4479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114451
X-RAY DIFFRACTIONf_angle_d1.5066019
X-RAY DIFFRACTIONf_dihedral_angle_d21.2441610
X-RAY DIFFRACTIONf_chiral_restr0.117675
X-RAY DIFFRACTIONf_plane_restr0.006751
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1487X-RAY DIFFRACTIONPOSITIONAL
12B1487X-RAY DIFFRACTIONPOSITIONAL0.273
21C611X-RAY DIFFRACTIONPOSITIONAL
22D611X-RAY DIFFRACTIONPOSITIONAL0.691
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.67-2.83730.38431500.31352667X-RAY DIFFRACTION90
2.8373-3.05630.33771550.29182820X-RAY DIFFRACTION94
3.0563-3.36380.30951700.24722816X-RAY DIFFRACTION94
3.3638-3.85040.23191460.21692813X-RAY DIFFRACTION92
3.8504-4.85060.21341430.17342739X-RAY DIFFRACTION90
4.8506-50.76480.19921330.18392605X-RAY DIFFRACTION83
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)
10.7171-0.0739-0.43820.2752-0.15940.94910.06470.02150.11140.06910.0456-0.0217-0.06190.07-0.11370.1875-0.0183-0.01960.1473-0.02710.236217.0163-17.204310.0061
20.5651-0.05960.53180.3110.0330.95860.06570.0093-0.0381-0.07370.0487-0.05680.05250.0627-0.11050.19570.00560.01180.141-0.03360.241916.8997-26.2902-9.9762
30.39520.54210.25710.77530.0721.66720.0981-0.0228-0.4194-0.0391-0.3596-0.58490.1988-0.19150.0710.252-0.102-0.11650.27060.11270.379412.8329-43.999232.8747
40.4787-0.2443-0.24170.1633-0.05771.03880.052-0.07830.2424-0.089-0.0757-0.2727-0.315-0.1912-0.03990.24660.06580.07380.17990.04110.248512.64150.8027-32.8355
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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