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- PDB-3h20: Crystal structure of primase RepB' -

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Basic information

Entry
Database: PDB / ID: 3h20
TitleCrystal structure of primase RepB'
ComponentsReplication protein B
KeywordsREPLICATION / primase / Nucleotidyltransferase / helix-bundle-domain / RSF1010
Function / homology
Function and homology information


RepB DNA-primase, N-terminal domain / RepB DNA-primase, N-terminal domain / RepB-like DNA primase domain / RepB DNA-primase N-terminal domain / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 - #50 / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Dna Ligase; domain 1 / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle ...RepB DNA-primase, N-terminal domain / RepB DNA-primase, N-terminal domain / RepB-like DNA primase domain / RepB DNA-primase N-terminal domain / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 - #50 / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Dna Ligase; domain 1 / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DIPHOSPHATE / Replication protein B
Similarity search - Component
Biological speciesPlasmid RSF1010 (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.99 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 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4215
Polymers35,9591
Non-polymers4624
Water4,558253
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Replication protein B
hetero molecules

A: Replication protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,84110
Polymers71,9172
Non-polymers9248
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3650 Å2
ΔGint-75 kcal/mol
Surface area30480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.740, 91.740, 83.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Replication protein B


Mass: 35958.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmid RSF1010 (others) / Gene: repb / Plasmid: pMS4708 / Production host: Escherichia coli (E. coli) / Strain (production host): SCS1
References: UniProt: Q52349, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DPO / DIPHOSPHATE


Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.64 % / Mosaicity: 0.284 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.3M ammonium sulfate, 22% (wt/vol) PEG monomethyl ether 2000, 5% (vol/vol) gamma-butyrolactone, 100mM sodium acetate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31
41
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-210.931
SYNCHROTRONESRF ID14-221.2557, 1.0442, 1.1406, 1.1402
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJul 4, 2006
ADSC QUANTUM 42CCDNov 26, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si111SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9311
21.25571
31.04421
41.14061
51.14021
Reflection

D res high: 2.7 Å / D res low: 50 Å

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2Num. obs% possible obs
3.6115.9628540.0390.991752896.5
3.9215.7703620.0390.951812099.9
3.9315.9709800.0370.981815999.9
3.5414.7614280.041.021749796
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.815099.210.021.1413.9
4.625.8110010.0270.8993.9
4.034.6210010.030.9573.9
3.664.0310010.0390.9733.9
3.43.6610010.061.0113.9
3.23.410010.0850.9913.9
3.043.210010.1470.9923.8
2.913.0499.610.2191.0053.5
2.82.9193.310.2490.9692.6
2.72.872.510.2740.931.8
5.815099.220.0210.893.9
4.625.8110020.0270.9593.9
4.034.6210020.0280.9473.9
3.664.0310020.0360.9673.9
3.43.6610020.0531.0053.9
3.23.410020.0760.9963.9
3.043.210020.1260.9713.9
2.913.0410020.1850.9383.9
2.82.9110020.2590.9033.9
2.72.899.920.3450.8993.6
5.81509930.0170.9463.9
4.625.8110030.0241.0244
4.034.6210030.0251.0343.9
3.664.0310030.0341.0423.9
3.43.6610030.0520.9713.9
3.23.410030.0750.9683.9
3.043.210030.1260.9843.9
2.913.0410030.1870.9783.9
2.82.9110030.2450.9343.9
2.72.810030.3390.9543.8
5.815099.240.0191.0033.8
4.625.8199.840.0280.9173.8
4.034.6299.940.0310.9973.7
3.664.0399.840.0421.0453.8
3.43.6610040.0661.0683.8
3.23.499.840.0991.073.6
3.043.299.940.1761.0133.8
2.913.0499.940.2671.0243.4
2.82.9197.640.3571.0043
2.72.864.440.3611.0731.9
ReflectionResolution: 1.98→50 Å / Num. all: 24819 / Num. obs: 24774 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.985→2.036 Å / % possible all: 100

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
XDSdata reduction
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.99→19.63 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.917 / SU B: 6.409 / SU ML: 0.096 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1026 4.1 %RANDOM
Rwork0.195 ---
all0.197 24819 --
obs0.197 24774 100 %-
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: 36.055 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.99→19.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2164 0 24 253 2441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222210
X-RAY DIFFRACTIONr_angle_refined_deg1.0961.9742982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2095283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76223.96101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88615374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9811522
X-RAY DIFFRACTIONr_chiral_restr0.0720.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021665
X-RAY DIFFRACTIONr_nbd_refined0.1820.2900
X-RAY DIFFRACTIONr_nbtor_refined0.2820.21511
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2183
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0990.221
X-RAY DIFFRACTIONr_mcbond_it0.5361.51481
X-RAY DIFFRACTIONr_mcangle_it0.83822234
X-RAY DIFFRACTIONr_scbond_it1.5363840
X-RAY DIFFRACTIONr_scangle_it2.5164.5748
LS refinement shellResolution: 1.985→2.036 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 7 -
Rwork0.2 1457 -
obs-1464 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)
10.8930.2555-0.03184.7569-2.35842.6421-0.01680.0295-0.1594-0.0431-0.1479-0.33940.11480.29140.1648-0.26740.01640.0176-0.1872-0.0089-0.189722.810938.575652.3602
28.8887-3.8048-16.06693.7437.073334.42590.07420.2216-0.231-0.9582-0.4026-0.28670.19120.21980.32850.18260.12260.1056-0.1840.0581-0.100424.089946.058721.1828
37.5641-1.13677.96482.1579-1.247613.17940.1876-0.1018-0.1933-0.0993-0.35560.34740.255-1.27560.168-0.1587-0.03080.03180.0437-0.162-0.045653.943126.81011.4134
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA5 - 177
2X-RAY DIFFRACTION2ALLA178 - 207
3X-RAY DIFFRACTION3ALLA219 - 307

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