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- PDB-2ygc: Structure of vaccinia virus D13 scaffolding protein -

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Basic information

Entry
Database: PDB / ID: 2ygc
TitleStructure of vaccinia virus D13 scaffolding protein
ComponentsRIFAMPICIN RESISTANCE PROTEIN
KeywordsVIRAL PROTEIN / VIRAL EVOLUTION
Function / homologyPoxvirus rifampicin-resistance / Poxvirus rifampicin resistance protein / response to antibiotic / identical protein binding / membrane / Scaffold protein OPG125
Function and homology information
Biological speciesVACCINIA VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.02 Å
AuthorsBahar, M.W. / Graham, S.C. / Stuart, D.I. / Grimes, J.M.
CitationJournal: Structure / Year: 2011
Title: Insights Into the Evolution of a Complex Virus from the Crystal Structure of Vaccinia Virus D13.
Authors: Bahar, M.W. / Graham, S.C. / Stuart, D.I. / Grimes, J.M.
History
DepositionApr 13, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Refinement description

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIFAMPICIN RESISTANCE PROTEIN
B: RIFAMPICIN RESISTANCE PROTEIN
C: RIFAMPICIN RESISTANCE PROTEIN


Theoretical massNumber of molelcules
Total (without water)192,9833
Polymers192,9833
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16090 Å2
ΔGint-107.1 kcal/mol
Surface area65090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.580, 190.580, 252.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein RIFAMPICIN RESISTANCE PROTEIN / 62 KDA PROTEIN / D13 SCAFFOLDING PROTEIN


Mass: 64327.750 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VACCINIA VIRUS / Strain: WESTERN RESERVE / Plasmid: POPINF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA PLYSS / References: UniProt: P68440
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 513 TO GLY ENGINEERED RESIDUE IN CHAIN B, ASP 513 TO GLY ...ENGINEERED RESIDUE IN CHAIN A, ASP 513 TO GLY ENGINEERED RESIDUE IN CHAIN B, ASP 513 TO GLY ENGINEERED RESIDUE IN CHAIN C, ASP 513 TO GLY
Sequence detailsSEQUENCE REPRESENTS D13 D513G MUTANT. SINGLE POINT MUTATION ENGINEERED AT RESIDUE 513 IN CHAINS A, ...SEQUENCE REPRESENTS D13 D513G MUTANT. SINGLE POINT MUTATION ENGINEERED AT RESIDUE 513 IN CHAINS A, B, AND C FROM ASPARTATE TO GLYCINE.

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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: 3.5 Å3/Da / Density % sol: 64 % / Description: NONE
Crystal growpH: 7.5 / Details: 4.0 M SODIUM FORMATE., pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9792
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 14, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→39.3 Å / Num. obs: 53583 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 20.8 % / Biso Wilson estimate: 80.51 Å2 / Rmerge(I) obs: 0.21 / Net I/σ(I): 16.9
Reflection shellResolution: 3→3.1 Å / Redundancy: 15.4 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 2 / % possible all: 98.6

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3.02→39.28 Å / Cor.coef. Fo:Fc: 0.9262 / Cor.coef. Fo:Fc free: 0.9052 / SU R Cruickshank DPI: 1.513 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.317 / SU Rfree Blow DPI: 0.295 / SU Rfree Cruickshank DPI: 0.302
Details: NCS REPRESENTATION, RESTRAINT LSSR (-AUTONCS). IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2029 2713 5.07 %RANDOM
Rwork0.17 ---
obs0.1717 53462 99.67 %-
Displacement parametersBiso mean: 62.45 Å2
Baniso -1Baniso -2Baniso -3
1-9.7536 Å20 Å20 Å2
2--9.7536 Å20 Å2
3----19.5071 Å2
Refine analyzeLuzzati coordinate error obs: 0.477 Å
Refinement stepCycle: LAST / Resolution: 3.02→39.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12900 0 0 79 12979
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00913194HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.117953HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6059SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes339HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1880HARMONIC5
X-RAY DIFFRACTIONt_it13194HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.05
X-RAY DIFFRACTIONt_other_torsion3.15
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1832SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies2HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14668SEMIHARMONIC4
LS refinement shellResolution: 3.02→3.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2975 182 4.78 %
Rwork0.243 3625 -
all0.2457 3807 -
obs--99.67 %
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)
10.1257-0.0726-0.0371-0.1257-0.01310-0.00340.00540.0018-0.00030.00010.0038-0.0023-0.00270.0032-0.02580.01270.01250.0126-0.00560.0059-28.9702-50.888128.7015
20.672-0.18830.9870.4283-0.24390.9056-0.0263-0.04310.01110.0806-0.0086-0.0295-0.1814-0.06870.0350.00470.00790.0434-0.0414-0.1416-0.050113.4923-54.487441.7629
31.1865-0.3926-0.84950.87650.42732.3887-0.0392-0.02390.13860.14190.0066-0.1064-0.00190.15370.0326-0.0285-0.00090.0011-0.0489-0.0707-0.067730.0861-59.57730.304
40.3139-0.394-0.05450.9782-0.55512.1840.03110.11630.0753-0.1464-0.0637-0.11760.26840.12190.0327-0.03940.03930.0320.0128-0.0396-0.080131.6385-76.1022-0.4057
50.2586-0.11760.48050.42560.10540.3596-0.0358-0.0993-0.07250.0840.07210.00440.07520.0517-0.03640.05680.09130.0288-0.0619-0.0031-0.03821.4817-80.27225.4848
6-0.07220.04590.01990.09370.11050.0076-0.0009-0.0014-0.003-0.00070.0014-0.0011-0.0042-0.0006-0.00050.0131-0.00060.0181-0.003-0.02120.010120.6857-39.582851.915
70.97090.30010.28521.4681-0.1560.2484-0.006-0.1233-0.01380.00560.05610.03030.10340.0087-0.05010.09510.04860.1517-0.0981-0.0408-0.09030.5243-75.602934.3322
80.5031-0.23020.6940.8432-0.36431.95810.0343-0.0309-0.2094-0.01730.03180.17010.227-0.0216-0.066-0.02580.01530.0385-0.0406-0.006-0.0686-2.397-80.506314.4819
90.99930.1698-0.40690.5811-0.39171.1839-0.00270.22350.0371-0.1025-0.10340.05240.1131-0.01360.1061-0.09370.0401-0.0210.0436-0.0089-0.0393-1.2798-59.4628-13.7362
100.5411-0.29980.29880.4640.1640.7762-0.0045-0.07040.0673-0.02740.05080.13860.0063-0.1861-0.0463-0.10510.00410.04830.0373-0.03520.006-14.888-61.531411.9456
11-0.0710.0339-0.06520.0955-0.08750.00020.0017-0.0008-0.0028-0.0011-0.0025-0.0010.00130.00050.00080.0159-0.0108-0.0064-0.01420.01290.00055.7215-92.904140.925
120.8127-0.42940.07690.04990.64650.2914-0.019-0.00610.08050.0607-0.08820.0901-0.0233-0.14930.1072-0.14250.07270.05490.11330.0195-0.0444-9.8871-51.271631.1451
131.37280.380.05770.9634-0.5970.8649-0.11820.01130.39650.04350.08310.1247-0.2308-0.20410.0352-0.06520.0990.0037-0.0765-0.03280.0072-3.5504-38.672417.2787
140.6899-0.0567-0.27130.61440.23072.0913-0.12690.25710.4044-0.02590.0808-0.0146-0.23090.17390.046-0.0894-0.082-0.0678-0.0760.10360.053227.1548-36.55320.6964
150.0623-0.22180.68840.617-0.19540.225-0.1629-0.02140.29970.17760.09240.0229-0.21020.03460.07050.04730.0283-0.0367-0.0951-0.11080.021216.2899-38.217431.666
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESIDUES 2 - 10)
2X-RAY DIFFRACTION2(CHAIN A AND RESIDUES 15 - 50)
3X-RAY DIFFRACTION3(CHAIN A AND RESIDUES 51 - 231)
4X-RAY DIFFRACTION4(CHAIN A AND RESIDUES 232 - 404)
5X-RAY DIFFRACTION5(CHAIN A AND RESIDUES 405 - 547)
6X-RAY DIFFRACTION6(CHAIN B AND RESIDUES 2 - 10)
7X-RAY DIFFRACTION7(CHAIN B AND RESIDUES 15 - 50)
8X-RAY DIFFRACTION8(CHAIN B AND RESIDUES 51 - 231)
9X-RAY DIFFRACTION9(CHAIN B AND RESIDUES 232 - 408)
10X-RAY DIFFRACTION10(CHAIN B AND RESIDUES 409 - 547)
11X-RAY DIFFRACTION11(CHAIN C AND RESIDUES 2 - 10)
12X-RAY DIFFRACTION12(CHAIN C AND RESIDUES 15 - 51)
13X-RAY DIFFRACTION13(CHAIN C AND RESIDUES 52 - 231)
14X-RAY DIFFRACTION14(CHAIN C AND RESIDUES 232 - 424)
15X-RAY DIFFRACTION15(CHAIN C AND RESIDUES 425 - 547)

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