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

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Basic information

Entry
Database: PDB / ID: 3dkx
TitleCrystal Structure of the replication initiator protein encoded on plasmid pMV158 (RepB), trigonal form, to 2.7 Ang resolution
ComponentsReplication protein repB
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, 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 / MAD / Resolution: 2.7 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 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Mar 20, 2024Group: 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 / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,15710
Polymers72,8613
Non-polymers2957
Water2,198122
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)146,31420
Polymers145,7236
Non-polymers59114
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area15970 Å2
ΔGint-168 kcal/mol
Surface area62670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.611, 85.611, 245.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B
32C

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPGLYGLY2AA135 - 204135 - 204
211ASPASPGLYGLY2BB135 - 204135 - 204
311ASPASPARGARG2CC135 - 203135 - 203
112TYRTYRPROPRO5AA8 - 378 - 37
212TYRTYRPROPRO5BB8 - 378 - 37
312TYRTYRPROPRO5CC8 - 378 - 37
122HISHISLEULEU5AA55 - 7855 - 78
222HISHISLEULEU5BB55 - 7855 - 78
322HISHISLEULEU5CC55 - 7855 - 78
132ASPASPPHEPHE5AA119 - 126119 - 126
232ASPASPPHEPHE5BB119 - 126119 - 126
332ASPASPPHEPHE5CC119 - 126119 - 126

NCS ensembles :
ID
1
2

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Components

#1: Protein Replication protein repB


Mass: 24287.105 Da / Num. of mol.: 3
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.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 5

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Sample preparation

CrystalDensity Matthews: 3.56 Å3/Da / Density % sol: 65.5 %
Description: the diffraction experiments are for native, Se-MET, Se-MET, K2PTCL4 soak and K2PTCL4 soak in order.
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10% PEG 8000, 100 mM CaCl2, 50mM TRIS HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
41001
51001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONESRF ID2911.0052
SYNCHROTRONESRF ID14-420.9792
SYNCHROTRONESRF BM1430.9791, 0.9686
SYNCHROTRONESRF ID2941.07207, 1.07244, 1.06736
ROTATING ANODERIGAKU51.54179
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDApr 23, 2004
ADSC QUANTUM 2102CCDApr 14, 2003
ADSC QUANTUM 2103CCDJul 12, 2003
ADSC QUANTUM 2104CCDFeb 23, 2006
MAR scanner 345 mm plate5IMAGE PLATEFeb 14, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111) monochromatorSINGLE WAVELENGTHMx-ray1
2SADMx-ray2
3MADMx-ray3
4MADMx-ray4
5SADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.00521
20.97921
30.97911
40.96861
51.072071
61.072441
71.067361
81.541791
ReflectionResolution: 2.7→24.95 Å / Num. all: 29602 / Num. obs: 29572 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 71.2 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.1
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.748 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4243 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ProDC(ESRF)data collection
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
DMphasing
DMMultiphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→24.95 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.889 / SU B: 25.159 / SU ML: 0.241 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.505 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; The isotropic atomic B values and ANISOU cards represent the full displacement of the atoms and therefore include the TLS component
RfactorNum. reflection% reflectionSelection details
Rfree0.27574 1499 5.1 %RANDOM
Rwork0.22814 ---
obs0.23048 28019 100 %-
all-29518 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.33 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å20.73 Å20 Å2
2--1.46 Å20 Å2
3----2.19 Å2
Refine analyzeLuzzati coordinate error obs: 0.399 Å
Refinement stepCycle: LAST / Resolution: 2.7→24.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4928 0 7 122 5057
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225024
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.9776775
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3875602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3124.73222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.25515969
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.3981518
X-RAY DIFFRACTIONr_chiral_restr0.0910.2771
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023650
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5131.53011
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.97524882
X-RAY DIFFRACTIONr_scbond_it1.22932013
X-RAY DIFFRACTIONr_scangle_it2.0814.51893
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A276tight positional0.040.05
12B276tight positional0.040.05
13C276tight positional0.050.05
11A284medium positional0.170.5
12B284medium positional0.150.5
13C284medium positional0.130.5
21A248medium positional0.220.5
22B248medium positional0.180.5
23C248medium positional0.20.5
21A262loose positional0.595
22B262loose positional0.625
23C262loose positional0.615
11A276tight thermal0.090.5
12B276tight thermal0.090.5
13C276tight thermal0.090.5
11A284medium thermal0.112
12B284medium thermal0.112
13C284medium thermal0.12
21A248medium thermal1.472
22B248medium thermal1.012
23C248medium thermal0.822
21A262loose thermal1.2810
22B262loose thermal0.910
23C262loose thermal0.8610
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 110 -
Rwork0.323 2016 -
obs--100 %
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)
13.9466-0.11360.13954.50611.95485.1931-0.3409-0.51210.49840.5056-0.15540.302-0.3992-0.5120.49630.16760.0799-0.05480.3593-0.16060.1229-49.210539.6207-26.7528
24.34520.0467-0.60351.1654-0.59732.70640.14630.04970.18010.0255-0.00910.0596-0.19-0.153-0.13720.0206-0.02240.00720.2980.00380.091-51.602533.0713-58.1871
32.08910.64410.30442.6941-0.52894.34070.2326-0.1229-0.0006-0.0955-0.25840.1667-0.21530.52430.02580.0589-0.0096-0.00950.28010.04440.026-30.284640.2065-81.1531
42.6574-0.0665-0.33691.8483-0.42072.7450.0086-0.1202-0.06820.16050.016-0.05710.1705-0.0571-0.02460.0939-0.0597-0.00650.06450.02880.0829-17.799317.2503-22.7529
50.47520.11930.25443.1033-0.33383.401-0.02220.0336-0.1192-0.00530.08810.03850.3166-0.3908-0.06590.0809-0.09990.010.12810.00520.1477-28.389911.1628-37.6464
61.61750.3469-0.57781.8775-0.58742.6403-0.11430.4043-0.1303-0.17040.10610.03050.3648-0.24180.00820.0791-0.08540.00740.187-0.05410.1118-22.417414.4173-55.7627
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 132
2X-RAY DIFFRACTION2B3 - 132
3X-RAY DIFFRACTION3C3 - 132
4X-RAY DIFFRACTION4A133 - 204
5X-RAY DIFFRACTION5B133 - 204
6X-RAY DIFFRACTION6C133 - 203

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