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

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Basic information

Entry
Database: PDB / ID: 2ygb
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 / membrane / identical protein binding / Scaffold protein OPG125
Function and homology information
Biological speciesVACCINIA VIRUS WESTERN RESERVE
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 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 1.1May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)191,8913
Polymers191,8913
Non-polymers00
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12950 Å2
ΔGint-90.7 kcal/mol
Surface area66310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.090, 190.090, 257.090
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: 63963.719 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VACCINIA VIRUS WESTERN RESERVE / Plasmid: POPINF / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): ROSETTA PLYSS / References: UniProt: P68440
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 3.5 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growpH: 7.5 / Details: 3.5 M SODIUM FORMATE., pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9782
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9782 Å / Relative weight: 1
ReflectionResolution: 2.8→46.2 Å / Num. obs: 64720 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 81.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 19
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 2.7 / % possible all: 95.5

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
xia2data reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→46.21 Å / Cor.coef. Fo:Fc: 0.9353 / Cor.coef. Fo:Fc free: 0.9179 / SU R Cruickshank DPI: 0.496 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.487 / SU Rfree Blow DPI: 0.256 / SU Rfree Cruickshank DPI: 0.261
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.206 3281 5.07 %RANDOM
Rwork0.1773 ---
obs0.1787 64720 96.47 %-
Displacement parametersBiso mean: 67.15 Å2
Baniso -1Baniso -2Baniso -3
1-8.3596 Å20 Å20 Å2
2--8.3596 Å20 Å2
3----16.7193 Å2
Refine analyzeLuzzati coordinate error obs: 0.359 Å
Refinement stepCycle: LAST / Resolution: 2.81→46.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12709 0 0 147 12856
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00913000HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0417691HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5964SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes333HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1855HARMONIC5
X-RAY DIFFRACTIONt_it13000HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.06
X-RAY DIFFRACTIONt_other_torsion3.02
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1795SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact13854SEMIHARMONIC4
LS refinement shellResolution: 2.81→2.88 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2949 263 5.63 %
Rwork0.2498 4411 -
all0.2523 4674 -
obs--96.47 %
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)
12.3110.5087-0.72070.40460.41810.7601-0.0329-0.0282-0.02240.0678-0.00090.12670.21020.08270.0337-0.03380.03840.0033-0.02220.157-0.0322-13.475754.692641.4405
21.0184-0.22560.36311.0962-0.63442.321-0.0297-0.1028-0.08710.10860.03330.18280.044-0.2268-0.0035-0.06750.0180.0304-0.05650.0521-0.0473-29.693159.484329.6725
30.7611-0.29330.07410.76860.27461.20010.09830.1872-0.074-0.1817-0.06370.0967-0.2289-0.3083-0.0345-0.00590.0917-0.0579-0.0204-0.0047-0.1216-30.461476.74851.3835
40.5917-0.13710.10.54430.04260.65350.0118-0.04660.04240.05260.06810.0153-0.1784-0.0821-0.07990.04050.0536-0.0149-0.03420.0088-0.0799-19.381580.387526.7529
51.67850.7584-0.87021.4799-0.3770.02610.0341-0.10660.1125-0.017-0.0135-0.0812-0.1129-0.0123-0.02050.11720.0169-0.0852-0.1379-0.0392-0.0741.403576.002733.2336
60.7597-0.1914-0.56180.88920.33752.984-0.0025-0.01140.2364-0.02560.0183-0.1465-0.30620.193-0.0158-0.00850.0165-0.0088-0.08650.009-0.08273.716780.537114.6121
71.4869-0.00460.60220.44190.26972.0657-0.01440.3165-0.0969-0.1372-0.0921-0.0244-0.1748-0.01060.1065-0.0640.05790.04780.002-0.0321-0.09631.890959.8375-13.945
80.2949-0.38-0.28370.45850.05680.7293-0.0297-0.04610.0397-0.00660.0723-0.114-0.06160.1175-0.0426-0.06760.00850.0080.04320.0186-0.027315.884361.209410.6148
90.9005-0.4182-0.14170.4615-0.32780.5367-0.06230.0331-0.06270.0585-0.0872-0.0972-0.00330.10870.1495-0.08720.08750.04940.115-0.0227-0.122510.648350.417330.5455
101.68250.14930.47480.69390.65541.6372-0.19270.0849-0.30460.06530.0330.03970.2940.23590.1596-0.02270.03110.0895-0.02970.0211-0.08474.10938.356216.8395
110.53060.0240.11310.3580.18181.9065-0.12280.2389-0.2720.0188-0.06510.14420.2581-0.31480.1879-0.0919-0.10290.07060.0275-0.1342-0.0275-26.259336.6466-0.0352
12-0.12470.0784-0.63420.55180.44740.6189-0.12180.0217-0.27520.1118-0.03910.06890.2921-0.01360.16090.00710.00110.0978-0.04970.06480.0189-15.984738.14231.9938
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 15 : 51
2X-RAY DIFFRACTION2CHAIN A AND RESID 52 : 224
3X-RAY DIFFRACTION3CHAIN A AND RESID 225 : 410
4X-RAY DIFFRACTION4CHAIN A AND RESID 411 : 547
5X-RAY DIFFRACTION5CHAIN B AND RESID 15 : 52
6X-RAY DIFFRACTION6CHAIN B AND RESID 53 : 231
7X-RAY DIFFRACTION7CHAIN B AND RESID 232 : 404
8X-RAY DIFFRACTION8CHAIN B AND RESID 405 : 548
9X-RAY DIFFRACTION9CHAIN C AND RESID 15 : 52
10X-RAY DIFFRACTION10CHAIN C AND RESID 53 : 232
11X-RAY DIFFRACTION11CHAIN C AND RESID 233 : 431
12X-RAY DIFFRACTION12CHAIN C AND RESID 432 : 547

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