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- PDB-2rh3: Crystal structure of plasmid pTiC58 VirC2 -

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Basic information

Entry
Database: PDB / ID: 2rh3
TitleCrystal structure of plasmid pTiC58 VirC2
ComponentsProtein virC2
KeywordsDNA BINDING PROTEIN / Ribbon-Helix-Helix / Protein / Crown gall tumor
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
VirC2, RHH domain / VirC2 / VirC2, C-terminal domain superfamily / VirC2 protein / Arc Repressor Mutant / Ribbon-helix-helix / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsLu, J. / Glover, J.N.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Agrobacterium tumefaciens VirC2 enhances T-DNA transfer and virulence through its C-terminal ribbon-helix-helix DNA-binding fold
Authors: Lu, J. / den Dulk-Ras, A. / Hooykaas, P.J. / Glover, J.N.
History
DepositionOct 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Feb 21, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein virC2


Theoretical massNumber of molelcules
Total (without water)13,4131
Polymers13,4131
Non-polymers00
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.374, 57.374, 33.935
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Protein virC2


Mass: 13413.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: GV3101(pMP90) / Gene: virC2 / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P07166
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.4 Å3/Da / Density % sol: 48.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.3.110.979602
SYNCHROTRONALS 8.3.121.115872
Detector
TypeIDDetector
ADSC QUANTUM 2101CCD
ADSC QUANTUM 3152CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9796021
21.1158721
ReflectionRedundancy: 3.6 % / Av σ(I) over netI: 13.7 / Number: 23945 / Rmerge(I) obs: 0.067 / Χ2: 1.1 / D res high: 2.9 Å / D res low: 30 Å / Num. obs: 6705 / % possible obs: 98.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.833080.110.0141.0033.7
6.237.838910.0311.013.6
5.456.2397.410.0460.9183.4
4.955.4597.910.0510.9433.5
4.64.9599.410.0570.9783.6
4.334.610010.071.1273.6
4.114.3399.710.0751.1033.6
3.934.1199.710.0791.1483.5
3.783.9310010.0841.0593.6
3.653.7899.710.11.1573.6
3.543.6510010.1121.1473.6
3.443.5410010.1351.1423.6
3.353.4410010.171.2243.6
3.273.3510010.2061.1493.6
3.193.2710010.2531.2153.6
3.123.1910010.3041.1983.6
3.063.1299.710.3561.1743.6
33.0610010.4371.1593.5
2.95310010.4550.9563.6
2.92.9599.710.5311.1893.5
ReflectionResolution: 1.7→30 Å / Num. all: 13804 / Num. obs: 13376 / % possible obs: 96.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.062 / Rsym value: 0.049 / Net I/σ(I): 18.6
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 18.6 / Num. unique all: 13804 / Rsym value: 0.049 / % possible all: 96.9

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se37.4990.430.76300.73
2Se39.1920.6290.6440.2820.34
3Se47.2590.880.5790.1490.323
Phasing dmFOM : 0.66 / FOM acentric: 0.66 / FOM centric: 0 / Reflection: 3191 / Reflection acentric: 3191 / Reflection centric: 0
Phasing dm shell
Resolution (Å)FOM FOM acentricReflectionReflection acentric
8.3-28.1650.940.94136136
5.2-8.30.880.88422422
4.1-5.20.850.85538538
3.6-4.10.770.77547547
3.1-3.60.560.56965965
2.9-3.10.330.33583583

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.08phasing
RESOLVE2.08phasing
REFMACrefinement
PDB_EXTRACT3data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.188 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: Hydrogens have been added in the riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.209 678 5.1 %RANDOM
Rwork0.183 ---
obs0.184 13368 96.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.536 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20.21 Å20 Å2
2--0.42 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms945 0 0 100 1045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221031
X-RAY DIFFRACTIONr_angle_refined_deg1.071.9741409
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4995137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.65822.544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40415179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.422159
X-RAY DIFFRACTIONr_chiral_restr0.0760.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02794
X-RAY DIFFRACTIONr_nbd_refined0.2070.2490
X-RAY DIFFRACTIONr_nbtor_refined0.3010.2737
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.272
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2350.211
X-RAY DIFFRACTIONr_mcbond_it0.6681.5659
X-RAY DIFFRACTIONr_mcangle_it1.12421051
X-RAY DIFFRACTIONr_scbond_it1.6783406
X-RAY DIFFRACTIONr_scangle_it2.684.5352
LS refinement shellResolution: 1.7→1.73 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 51 -
Rwork0.265 814 -
all-865 -
obs--85.39 %
Refinement TLS params.Method: refined / Origin x: 23.3167 Å / Origin y: 33.0465 Å / Origin z: 11.6392 Å
111213212223313233
T0.018 Å20.0363 Å20.0175 Å2--0.0582 Å20.0119 Å2---0.0663 Å2
L1.3243 °2-1.0644 °20.281 °2-3.6129 °21.1027 °2--0.9714 °2
S-0.0312 Å °-0.0742 Å °0.0049 Å °-0.0422 Å °0.0211 Å °0.1778 Å °-0.2458 Å °-0.1795 Å °0.0101 Å °

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