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- PDB-3dky: Crystal Structure of the replication initiator protein encoded on... -

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Basic information

Entry
Database: PDB / ID: 3dky
TitleCrystal Structure of the replication initiator protein encoded on plasmid pMV158 (RepB), tetragonal form, to 3.6 Ang resolution
ComponentsReplication protein repBDNA replication
KeywordsREPLICATION / Replication initiation / Plasmid replication / Nuclease / Hexamer / Flexible nuclease domains / DNA replication / Plasmid / REPLICATION INITIATOR
Function / homology
Function and homology information


DNA topoisomerase activity / extrachromosomal circular DNA / DNA replication / DNA binding / identical protein binding
Similarity search - Function
Plasmid replication protein / Replication Protein E1; Chain: A, - #30 / Plasmid replication protein / Plasmid replication protein, C-terminal domain superfamily / Plasmid replication protein / Replication Protein E1; Chain: A, / Arc Repressor Mutant, subunit A / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Replication protein RepB
Similarity search - Component
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsBoer, D.R. / Ruiz-Maso, J.A. / Blanco, A.G. / Vives-Llacer, M. / Uson, I. / Gomis-Ruth, F.X. / Espinosa, M. / Del Solar, G. / Coll, M.
CitationJournal: Embo J. / Year: 2009
Title: Plasmid replication initiator RepB forms a hexamer reminiscent of ring helicases and has mobile nuclease domains
Authors: Boer, D.R. / Ruiz-Maso, J.A. / Lopez-Blanco, J.R. / Blanco, A.G. / Vives-Llacer, M. / Chacon, P. / Uson, I. / Gomis-Ruth, F.X. / Espinosa, M. / Llorca, O. / del Solar, G. / Coll, M.
History
DepositionJun 26, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Replication protein repB
B: Replication protein repB
C: Replication protein repB
D: Replication protein repB
E: Replication protein repB
F: Replication protein repB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,94210
Polymers145,7236
Non-polymers2204
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.460, 91.460, 227.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
12A
22D
32F
42E
52B
62C
13B
23D
33F
14A
24C
34E

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and resid 135:203A135 - 203
211chain B and resid 135:203B135 - 203
311chain C and resid 135:203C135 - 203
411chain D and resid 135:203D135 - 203
511chain E and resid 135:203E135 - 203
611chain F and resid 135:203F135 - 203
112chain A and (resid 4:129 or resid 301)A0
212chain D and (resid 4:129 or resid 301)D0
312chain F and (resid 4:129 or resid 301)F0
412chain E and (resid 4:129 or resid 301)E0
512chain B and (resid 4:129 or resid 301)B0
612chain C and (resid 4:129 or resid 301)C0
113chain B and resid 130:134B130 - 134
213chain D and resid 130:134D130 - 134
313chain F and resid 130:134F130 - 134
114chain A and resid 130:134A130 - 134
214chain C and resid 130:134C130 - 134
314chain E and resid 130:134E130 - 134

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein
Replication protein repB / DNA replication


Mass: 24287.105 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Gene: repB / Plasmid details: repB (plasmid pMV158) / Plasmid: pGEM-T / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P13921
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn

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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: 3.26 Å3/Da / Density % sol: 62.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 10% PEG 4000, 0.2mM MgCl2, 50mM CHES, pH 9, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.005 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 23, 2004
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 3.6→25 Å / Num. obs: 21350 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 10.95
Reflection shellResolution: 3.6→3.85 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 3.01 / Num. measured all: 7763 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ProDC(ESRF)data collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
AMoREphasing
MOLREPphasing
PHENIX1.4_4refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DKX

3dkx


Resolution: 3.6→19.571 Å / Occupancy max: 1 / Occupancy min: 1 / SU B: 64.622 / SU ML: -0 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 24.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2567 1098 5.14 %RANDOM
Rwork0.2234 20252 --
obs0.2251 21350 99.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.996 Å2 / ksol: 0.284 e/Å3
Displacement parametersBiso max: 317.99 Å2 / Biso mean: 158.604 Å2 / Biso min: 90.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.741 Å20 Å20 Å2
2--0.741 Å2-0 Å2
3----1.482 Å2
Refine analyzeLuzzati coordinate error obs: 0.827 Å
Refinement stepCycle: LAST / Resolution: 3.6→19.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9459 0 4 0 9463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0189644
X-RAY DIFFRACTIONf_angle_d1.6713025
X-RAY DIFFRACTIONf_chiral_restr0.0931492
X-RAY DIFFRACTIONf_plane_restr0.0051617
X-RAY DIFFRACTIONf_dihedral_angle_d20.0583528
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A560X-RAY DIFFRACTIONPOSITIONAL0.09
12B560X-RAY DIFFRACTIONPOSITIONAL0.09
13C560X-RAY DIFFRACTIONPOSITIONAL0.098
14D560X-RAY DIFFRACTIONPOSITIONAL0.086
15E560X-RAY DIFFRACTIONPOSITIONAL0.089
16F560X-RAY DIFFRACTIONPOSITIONAL0.078
21A936X-RAY DIFFRACTIONPOSITIONAL0.089
22D936X-RAY DIFFRACTIONPOSITIONAL0.089
23F937X-RAY DIFFRACTIONPOSITIONAL0.093
24E863X-RAY DIFFRACTIONPOSITIONAL0.086
25B1027X-RAY DIFFRACTIONPOSITIONAL0.093
26C1027X-RAY DIFFRACTIONPOSITIONAL0.091
31B45X-RAY DIFFRACTIONPOSITIONAL0.1
32D45X-RAY DIFFRACTIONPOSITIONAL0.1
33F45X-RAY DIFFRACTIONPOSITIONAL0.105
41A45X-RAY DIFFRACTIONPOSITIONAL0.093
42C45X-RAY DIFFRACTIONPOSITIONAL0.093
43E45X-RAY DIFFRACTIONPOSITIONAL0.078
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.76280.32821440.32882513X-RAY DIFFRACTION100
3.7628-3.95960.31261590.30142531X-RAY DIFFRACTION100
3.9596-4.20540.32981430.2692495X-RAY DIFFRACTION100
4.2054-4.52640.27351230.2362556X-RAY DIFFRACTION100
4.5264-4.97510.22721370.21562545X-RAY DIFFRACTION100
4.9751-5.67960.2151290.20462551X-RAY DIFFRACTION100
5.6796-7.09850.24651220.20462548X-RAY DIFFRACTION100
7.0985-19.57090.20381410.1742513X-RAY DIFFRACTION98
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)
18.66120.10841.880510.52140.53272.7389-0.2635-0.0355-0.2492-0.7526-0.61190.62640.1837-1.44070.00370.4614-0.0317-0.05221.0959-0.70060.9578-9.759823.1084-7.8916
28.6352-1.29975.80458.78210.32053.85730.1073-0.9102-1.0641-0.5721-0.8751.39980.81180.0499-0.00810.6213-0.21170.05930.8119-0.48730.41563.970110.2132-5.3808
36.7795-2.09935.97839.2773.07465.68210.0897-0.5125-0.10960.8054-0.1938-0.21870.3972-0.0290.00030.642-0.13550.01570.4587-0.15980.269118.828813.98366.1162
48.3792-4.74153.61386.4112.68288.96340.2569-0.33130.24820.9231-0.372-0.5998-0.89640.10750.00440.8798-0.0097-0.15350.4187-0.30640.546420.21230.712715.2396
57.7557-0.88422.34.02064.27055.339-0.21230.14640.83390.26310.0483-0.2884-0.5085-0.90130.0020.6884-0.02480.00720.7345-0.54781.07576.259643.784512.8172
67.0081-1.42812.29197.3423.98993.66080.1005-0.1750.64750.3035-0.61910.9150.22-1.41050.0020.5467-0.04790.06661.1299-0.6831.1802-8.603339.94711.3163
711.1205-2.69993.81955.17431.38964.4648-2.30251.61272.1223-0.61180.2594-0.3686-2.69331.7968-1.4704-1.15840.38361.03250.2759-0.2425-0.535513.423319.1758-39.0564
86.59081.29932.07182.19830.18694.5508-0.3496-0.7092-0.3112-0.11570.4761-1.53470.87210.75530.32210.07660.1130.36370.55150.08250.334136.01363.0952-23.0698
93.4022-3.8547-1.20650.69632.25662.08660.39910.2650.7111-0.09010.2347-0.2342-0.21570.79960.00010.6511-0.28430.33831.1546-0.45991.06548.574135.4937-8.067
102.6779-3.5832-1.35164.23811.57092.7610.2857-0.09711.0661-0.22080.8154-2.2093-0.6651.0921-0.00161.5412-0.12250.33321.2003-0.41032.236540.425360.78989.242
11-1.65650.69550.74572.177-3.53380.5989-0.28020.85521.0691-0.0301-0.116-0.1474-0.97380.480.00072.3908-0.3965-0.30832.0593-0.08992.48922.349963.4472-18.5613
12-0.6636-0.72190.8421-0.1082.30251.05850.03340.14531.32620.1357-0.18520.2931-1.56980.3914-0.00571.0789-0.22040.28611.6625-0.46081.3306-18.343243.7841-31.6714
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 135:203A135 - 203
2X-RAY DIFFRACTION2chain B and resid 135:203B135 - 203
3X-RAY DIFFRACTION3chain C and resid 135:203C135 - 203
4X-RAY DIFFRACTION4chain D and resid 135:203D135 - 203
5X-RAY DIFFRACTION5chain E and resid 135:203E135 - 203
6X-RAY DIFFRACTION6chain F and resid 135:203F135 - 203
7X-RAY DIFFRACTION7chain A and (resid 4:134 or resid 301)A0
8X-RAY DIFFRACTION8chain B and (resid 4:134 or resid 301)B0
9X-RAY DIFFRACTION9chain C and (resid 4:134 or resid 301)C0
10X-RAY DIFFRACTION10chain D and (resid 4:134 or resid 301)D0
11X-RAY DIFFRACTION11chain E and (resid 4:134 or resid 301)E0
12X-RAY DIFFRACTION12chain F and (resid 4:134 or resid 301)F0

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