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- PDB-4u87: Crystal structure of the Ba-soaked C2 crystal form of pMV158 repl... -

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Basic information

Entry
Database: PDB / ID: 4u87
TitleCrystal structure of the Ba-soaked C2 crystal form of pMV158 replication initiator RepB (P3221 space group)
ComponentsReplication protein RepB
KeywordsREPLICATION / DNA 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, origin binding domain / 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: 3.8 Å
AuthorsBoer, D.R. / Ruiz Maso, J.A. / del Solar, G. / Coll, M.
Funding support Spain, 4items
OrganizationGrant numberCountry
Ministerio de Ciencia e InnovacionBFU2008-02372/BMC Spain
Ministerio de Ciencia e InnovacionBFU2011-22588 Spain
Generalitat de CatalunyaSGR2009-1309 Spain
European UnionSILVER, No. 260644
CitationJournal: Sci Rep / Year: 2016
Title: Conformational plasticity of RepB, the replication initiator protein of promiscuous streptococcal plasmid pMV158.
Authors: Boer, D.R. / Ruiz-Maso, J.A. / Rueda, M. / Petoukhov, M.V. / Machon, C. / Svergun, D.I. / Orozco, M. / Del Solar, G. / Coll, M.
History
DepositionAug 1, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Dec 20, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,36818
Polymers72,8613
Non-polymers1,50715
Water00
1
A: Replication protein RepB
B: Replication protein RepB
C: Replication protein RepB
hetero molecules

A: Replication protein RepB
B: Replication protein RepB
C: Replication protein RepB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,73736
Polymers145,7236
Non-polymers3,01430
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area19410 Å2
ΔGint-257 kcal/mol
Surface area60700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.800, 85.800, 246.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
SymmetryHelical symmetry: (Circular symmetry: 2 / Dyad axis: no)
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
32

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain C and (resid 135:203)
211chain B and (resid 135:203)
311chain A and (resid 135:136 or resid 138:203)
112chain C and (resid 4:129 or resid 301)
212chain B and (resid 4:129 or resid 301)
312chain A and (resid 4:129 or resid 301)

NCS ensembles :
ID
1
2

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Components

#1: Protein Replication protein RepB / Replication Initator RepB


Mass: 24287.105 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: plasmid pMV158 / Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Gene: repB / Plasmid: pGEM-T / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P13921
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ba

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.59 Å3/Da / Density % sol: 65.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 12% PEG 8000, 100mM BaCl2, 50mM TRIS HCl, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 2.0702 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 16, 2005
RadiationMonochromator: double crystal (Si111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.0702 Å / Relative weight: 1
ReflectionResolution: 3.8→19.77 Å / Num. obs: 19844 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 7.54 % / Biso Wilson estimate: 67 Å2 / Rmerge(I) obs: 0.236 / Net I/σ(I): 7.54
Reflection shellResolution: 3.8→4 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.731 / Mean I/σ(I) obs: 2.82 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.6_289)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DKX

3dkx


Resolution: 3.8→19.77 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2371 968 4.88 %From 3DKX entry
Rwork0.2049 ---
obs0.2065 19841 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.59 Å2 / ksol: 0.278 e/Å3
Displacement parametersBiso mean: 109 Å2
Baniso -1Baniso -2Baniso -3
1-3.3389 Å2-0 Å20 Å2
2--3.3389 Å2-0 Å2
3----6.6777 Å2
Refinement stepCycle: LAST / Resolution: 3.8→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4839 0 15 0 4854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014933
X-RAY DIFFRACTIONf_angle_d1.1686656
X-RAY DIFFRACTIONf_dihedral_angle_d13.7041818
X-RAY DIFFRACTIONf_chiral_restr0.067761
X-RAY DIFFRACTIONf_plane_restr0.003824
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11C560X-RAY DIFFRACTIONPOSITIONAL
12B560X-RAY DIFFRACTIONPOSITIONAL0.046
13A551X-RAY DIFFRACTIONPOSITIONAL0.05
21C1027X-RAY DIFFRACTIONPOSITIONAL
22B1027X-RAY DIFFRACTIONPOSITIONAL0.046
23A946X-RAY DIFFRACTIONPOSITIONAL0.041
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8001-3.99890.33421370.29462703X-RAY DIFFRACTION100
3.9989-4.24710.29461390.24812707X-RAY DIFFRACTION100
4.2471-4.57130.2551430.20052692X-RAY DIFFRACTION100
4.5713-5.02450.21751340.19152705X-RAY DIFFRACTION100
5.0245-5.7360.22031360.17832696X-RAY DIFFRACTION100
5.736-7.1690.21161440.19082687X-RAY DIFFRACTION100
7.169-19.770.18991350.1762683X-RAY DIFFRACTION100
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)
10.2291-0.15790.08160.51020.24180.1928-0.1683-0.73770.56680.6331-0.0370.5474-0.6486-0.7309-0.00121.16540.17470.13621.6784-0.22241.3137-47.891638.1846-27.7513
20.5779-0.2449-0.27111.0586-0.51340.4249-0.00110.2570.082-0.01650.1370.2293-0.1214-0.6081-0.00040.4428-0.09520.00921.49560.11960.8439-51.500932.9344-58.0791
30.7777-0.88510.05281.84030.13830.56740.058-0.17350.0154-0.0566-0.40620.2567-0.16220.8810.0010.54570.0102-0.01921.15710.27190.6983-30.290340.3373-81.4125
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 3:134 or resid 301)
2X-RAY DIFFRACTION2chain B and (resid 3:134 or resid 301)
3X-RAY DIFFRACTION3chain C and (resid 3:134 or resid 301)

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