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- PDB-3sam: Structure of D13, the scaffolding protein of vaccinia virus (muta... -

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Basic information

Entry
Database: PDB / ID: 3sam
TitleStructure of D13, the scaffolding protein of vaccinia virus (mutant D513G)
ComponentsRifampicin resistance protein
KeywordsVIRAL PROTEIN / Double-barrel / jelly-roll / Scaffolding protein / structural protein / rifampicin-resistance protein / Surface of the immature virions and viral crescents
Function / homologyPoxvirus rifampicin-resistance / Poxvirus rifampicin resistance protein / response to antibiotic / identical protein binding / membrane / FORMIC ACID / Scaffold protein OPG125
Function and homology information
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.55 Å
AuthorsCoulibaly, F.
CitationJournal: Plos Pathog. / Year: 2011
Title: Membrane remodeling by the double-barrel scaffolding protein of poxvirus.
Authors: Hyun, J.K. / Accurso, C. / Hijnen, M. / Schult, P. / Pettikiriarachchi, A. / Mitra, A.K. / Coulibaly, F.
History
DepositionJun 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 19, 2011Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Rifampicin resistance protein
B: Rifampicin resistance protein
C: Rifampicin resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,30110
Polymers194,9783
Non-polymers3227
Water11,259625
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18300 Å2
ΔGint-117 kcal/mol
Surface area64140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.630, 189.630, 255.130
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


Mass: 64992.809 Da / Num. of mol.: 3 / Mutation: D513G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Strain: Western Reserve / Gene: D13, D13L, VACWR118 / Plasmid: pPROEx-Hta / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P68440
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 625 / 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: 3.4 Å3/Da / Density % sol: 63.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.3M Na formate, 100mM Bis-Tris pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953689 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 16, 2011
RadiationMonochromator: Double crystal monochromator with sagitally bent 2nd crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953689 Å / Relative weight: 1
ReflectionResolution: 2.55→20 Å / Num. all: 88239 / Num. obs: 87870 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 10.9 % / Biso Wilson estimate: 64.97 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 26.25
Reflection shellResolution: 2.55→2.62 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.1017 / Mean I/σ(I) obs: 2.25 / Num. unique all: 6430 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
BUSTER2.8.0refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.55→17.99 Å / Cor.coef. Fo:Fc: 0.9524 / Cor.coef. Fo:Fc free: 0.9414
Isotropic thermal model: Individual B factors with coupling of bonded atoms
Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2008 4412 5.02 %RANDOM
Rwork0.175 ---
all0.1763 87867 --
obs0.1763 87515 99.6 %-
Displacement parametersBiso mean: 53.49 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.282 Å
Refinement stepCycle: LAST / Resolution: 2.55→17.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12840 0 21 625 13486
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01131772
X-RAY DIFFRACTIONt_angle_deg1.13179252
X-RAY DIFFRACTIONt_dihedral_angle_d60222
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes3272
X-RAY DIFFRACTIONt_gen_planes18875
X-RAY DIFFRACTIONt_it1317720
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.59
X-RAY DIFFRACTIONt_other_torsion2.87
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion18335
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact152744
LS refinement shellResolution: 2.55→2.62 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2732 347 5.41 %
Rwork0.2323 6070 -
all0.2345 6417 -
obs-6417 99.9 %

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