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- PDB-3h25: Crystal structure of the catalytic domain of primase Repb' in com... -

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Basic information

Entry
Database: PDB / ID: 3h25
TitleCrystal structure of the catalytic domain of primase Repb' in complex with initiator DNA
Components
  • Replication protein B
  • SINGLE STRANDED INITIATOR DNA (SSIA)
KeywordsREPLICATION/DNA / PROTEIN-DNA-COMPLEX / HAIRPIN DNA / MIXED ALPHA-BETA FOLD / PRIMASE / RSF1010 / REPLICATION / REPLICATION-DNA COMPLEX
Function / homology
Function and homology information


RepB-like DNA primase domain / : / RepB DNA-primase N-terminal domain / RepB DNA-primase C-terminal helical domain / Single helix bin / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Replication protein B
Similarity search - Component
Biological speciesPlasmid RSF1010 (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGeibel, S. / Banchenko, S. / Engel, M. / Lanka, E. / Saenger, W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structure and function of primase RepB' encoded by broad-host-range plasmid RSF1010 that replicates exclusively in leading-strand mode
Authors: Geibel, S. / Banchenko, S. / Engel, M. / Lanka, E. / Saenger, W.
History
DepositionApr 14, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Replication protein B
C: SINGLE STRANDED INITIATOR DNA (SSIA)


Theoretical massNumber of molelcules
Total (without water)33,3952
Polymers33,3952
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.350, 85.350, 68.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Replication protein B


Mass: 25125.143 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, UNP RESIDUES 1-212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmid RSF1010 (others) / Gene: repb / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q52349
#2: DNA chain SINGLE STRANDED INITIATOR DNA (SSIA)


Mass: 8270.298 Da / Num. of mol.: 1 / Fragment: SINGLE STRANDED INITIATOR DNA, GB 2701-2727 / Source method: obtained synthetically / Details: Synthetic DNA / References: GenBank: 152577
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 1.88 Å3/Da / Density % sol: 34.52 %
Crystal growpH: 5
Details: 0.2M AMMONIUM CITRATE, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 5, 2007 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.7→19 Å / Num. all: 7400 / Num. obs: 7215 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rsym value: 0.111 / Net I/σ(I): 16.51
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 5.64 / Rsym value: 0.394 / % possible all: 95

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.3.0040refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CATALYTIC DOMAIN OF PDB 3H20, MODEL OF IDEAL B-DNA

3h20


Resolution: 2.7→19 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.863 / SU B: 30.309 / SU ML: 0.285 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.401 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.274 368 5 %RANDOM
Rwork0.224 ---
obs0.226 6997 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2--0.36 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1417 546 0 24 1987
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0212049
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9472.292887
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6055186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.97724.85770
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.16315236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3211513
X-RAY DIFFRACTIONr_chiral_restr0.0510.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021395
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1580.2768
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.280.21334
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.271
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1250.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0680.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1981.5954
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.35321466
X-RAY DIFFRACTIONr_scbond_it0.33331438
X-RAY DIFFRACTIONr_scangle_it0.6584.51421
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 26 -
Rwork0.28 497 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 10.4478 Å / Origin y: 16.5103 Å / Origin z: -10.3449 Å
111213212223313233
T-0.0096 Å20.012 Å20.0041 Å2--0.0394 Å20.004 Å2--0.0008 Å2
L1.8203 °2-0.4026 °2-0.9693 °2-0.5064 °20.2647 °2--1.4252 °2
S-0.021 Å °-0.0488 Å °-0.0944 Å °-0.0278 Å °-0.0313 Å °-0.0443 Å °0.0784 Å °0.0602 Å °0.0524 Å °

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