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- PDB-1hkq: PPS10 plasmid DNA replication initiator protein RepA. Replication... -

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Basic information

Entry
Database: PDB / ID: 1hkq
TitlePPS10 plasmid DNA replication initiator protein RepA. Replication inactive, dimeric N-terminal domain.
ComponentsREPLICATION PROTEIN
KeywordsDNA BINDING PROTEIN / WINGED-HELIX / PPS10 PLASMID / REPLICATION INITIATOR DIMER.
Function / homology
Function and homology information


DNA replication initiation / DNA-directed DNA polymerase activity / identical protein binding
Similarity search - Function
Initiator Rep protein / Initiator Replication protein, WH1 / Initiator Rep protein, WH2 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BENZOIC ACID / : / PHOSPHATE ION / Replication protein
Similarity search - Component
Biological speciesPSEUDOMONAS SAVASTANOI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.75 Å
AuthorsGiraldo, R. / Fernandez-Tornero, C. / Evans, P.R. / Diaz-Orejas, R. / Romero, A.
Citation
Journal: Nat.Struct.Biol. / Year: 2003
Title: A Conformational Switch between Transcriptional Repression and Replication Initiation in Repa Dimerization Domain
Authors: Giraldo, R. / Fernandez-Tornero, C. / Evans, P.R. / Diaz-Orejas, R. / Romero, A.
#1: Journal: J.Biol.Chem. / Year: 2003
Title: Structural Changes in Repa, a Plasmid Replication Initiator, Upon Binding to Origin DNA
Authors: Diaz-Lopez, T. / Lages-Gonzalo, M. / Serrano-Lopez, A. / Alfonso, C. / Rivas, G. / Diaz-Orejas, R. / Giraldo, R.
#2: Journal: Fems Microbiol.Rev. / Year: 2003
Title: Common Domains in the Initiators of DNA Replication in Bacteria, Archaea and Eukarya: Combined Structural, Functional and Phylogenetic Perspectives
Authors: Giraldo, R.
#3: Journal: Embo J. / Year: 1998
Title: Protein Domains and Conformational Changes in the Activation of Repa, a DNA Replication Initiator
Authors: Giraldo, R. / Andreu, J.M. / Diaz-Orejas, R.
#4: Journal: J.Mol.Biol. / Year: 1992
Title: Genetic and Functional Analysis of the Basic Replicon of Pps10, a Plasmid Specific for Pseudomonas Isolated from Pseudomonas Syringae, Patovar Savastanoi
Authors: Nieto, C. / Giraldo, R. / Fernandez-Tresguerres, M.E. / Diaz, R.
History
DepositionMar 11, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 27, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Apr 10, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant
Revision 1.5Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / 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 / _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_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_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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: REPLICATION PROTEIN
B: REPLICATION PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,30513
Polymers30,3612
Non-polymers1,94411
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.866, 55.533, 96.073
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.05164, 0.99822, 0.02989), (0.99745, 0.05008, 0.05089), (0.0493, 0.03245, -0.99826)
Vector: -15.37287, 11.53942, 70.66085)

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Components

#1: Protein REPLICATION PROTEIN / REPA


Mass: 15180.649 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN DIMER, RESIDUES 2-133
Source method: isolated from a genetically manipulated source
Details: PPS10 PLASMID DNA REPLICATION INITIATOR, REPLICATION INACTIVE, DIMERIC SPECIES
Source: (gene. exp.) PSEUDOMONAS SAVASTANOI (bacteria) / Plasmid: PRG-RECA-NHIS / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): SG22097 / References: UniProt: Q52546
#2: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCLONED REPA STARTS WITH A SINGLE MET RESIDUE

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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: 2.26 Å3/Da / Density % sol: 45.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: VAPOUR DIFFUSION (HANGING DROPS), WELLS: 500 MICROLITRES (14% PEG4000, 6% MPD), DROPS: 5 MICROLITRES PROTEIN (5 MG/ML IN 50 MM K2HPO4/ KH2PO4, PH= 6.2),5 MICROLITRES WELL SOL. PLUS 1 ...Details: VAPOUR DIFFUSION (HANGING DROPS), WELLS: 500 MICROLITRES (14% PEG4000, 6% MPD), DROPS: 5 MICROLITRES PROTEIN (5 MG/ML IN 50 MM K2HPO4/ KH2PO4, PH= 6.2),5 MICROLITRES WELL SOL. PLUS 1 MICROLITRE OF P-CL-MERCURIBENZOATE (=1 MM IN WATER), THIN LARGE CRYSTAL PRISMS APPEAR AT 295 DEGREES KELVIN IN 1 MONTH., pH 6.20
Crystal grow
*PLUS
Temperature: 295 K / pH: 6.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
114 %(w/v)PEG40001reservoir
26 %(v/v)MPD1reservoir
35 mg/mlprotein1drop
450 mMpotassium phosphate1droppH6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.0090, 1.0120
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0091
21.0121
ReflectionResolution: 2.75→48.2 Å / Num. obs: 8343 / % possible obs: 97.7 % / Observed criterion σ(I): 2.1 / Redundancy: 5.2 % / Biso Wilson estimate: 45.9 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 8
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.1 / % possible all: 97.8
Reflection
*PLUS
Highest resolution: 2.75 Å / Lowest resolution: 48.2 Å / Num. measured all: 44839 / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
% possible obs: 97.8 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
SHARPphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.75→27.89 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1025607.14 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE ELECTRON DENSITY FOR RESIDUES SER B36 - LYS B42 IN CHAIN B IS DISCONTINUOUS, INTERPRETED TO BE PARTIALLY DISORDERED. THUS IT HAS BEEN MODELLED BASED ON STEREOCHEMICAL RESTRAINTS.
RfactorNum. reflection% reflectionSelection details
Rfree0.272 806 10.9 %RANDOM
Rwork0.238 ---
obs0.238 7421 96.6 %-
Solvent computationSolvent model: FLAT / Bsol: 27.2205 Å2 / ksol: 0.305183 e/Å3
Displacement parametersBiso mean: 48.1 Å2
Baniso -1Baniso -2Baniso -3
1-5.08 Å20 Å20 Å2
2--6.99 Å20 Å2
3----12.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.75→27.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2026 0 31 30 2087
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.75→2.92 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.378 125 10.1 %
Rwork0.342 1110 -
obs--97.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4BENZ_NO.PARAMBENZ_NO.TOP
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89
LS refinement shell
*PLUS
Lowest resolution: 2.9 Å

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