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- PDB-3saq: Structure of D13, the scaffolding protein of vaccinia virus -

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Basic information

Entry
Database: PDB / ID: 3saq
TitleStructure of D13, the scaffolding protein of vaccinia virus
ComponentsRifampicin resistance protein
KeywordsVIRAL PROTEIN / double-barrel / jelly-roll / Scaffolding protein / structural protein / rifampicin-resistance protein / Surface of the immature virions and crescents
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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.51 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 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)130,1022
Polymers130,1022
Non-polymers00
Water0
1
A: Rifampicin resistance protein

A: Rifampicin resistance protein

A: Rifampicin resistance protein


Theoretical massNumber of molelcules
Total (without water)195,1533
Polymers195,1533
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5170 Å2
ΔGint-40 kcal/mol
Surface area61590 Å2
MethodPISA
2
B: Rifampicin resistance protein

B: Rifampicin resistance protein

B: Rifampicin resistance protein


Theoretical massNumber of molelcules
Total (without water)195,1533
Polymers195,1533
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area5430 Å2
ΔGint-41 kcal/mol
Surface area62230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.130, 125.130, 370.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Rifampicin resistance protein / 62 kDa protein


Mass: 65050.840 Da / Num. of mol.: 2
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

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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: 2.15 Å3/Da / Density % sol: 42.72 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: 200mM NaBr, 20% PEG3550, Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2010
RadiationMonochromator: Double crystal monochromator with sagitally bent 2nd crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 3.5→30 Å / Num. all: 14242 / Num. obs: 13943 / % possible obs: 97.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 58.89 Å2 / Rmerge(I) obs: 0.156 / Net I/σ(I): 10.4
Reflection shellResolution: 3.5→3.62 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2.19 / Num. unique all: 1391 / % possible all: 98.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
BUSTER2.8.0refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2SAM

2sam


Resolution: 3.51→26.81 Å / Cor.coef. Fo:Fc: 0.7685 / Cor.coef. Fo:Fc free: 0.6864 / Isotropic thermal model: TLS with one group per chain / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: ONLY TLS REFINEMENT (2 GROUPS). NO INDIVIDUAL B REFINEMENT DUE TO THE LOW RESOLUTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2565 699 5.01 %RANDOM
Rwork0.2452 ---
all0.2457 13943 --
obs0.2457 13650 97.8 %-
Displacement parametersBiso mean: 99.15 Å2
Baniso -1Baniso -2Baniso -3
1-29.2802 Å20 Å20 Å2
2--29.2802 Å20 Å2
3----58.5605 Å2
Refine analyzeLuzzati coordinate error obs: 0.79 Å
Refinement stepCycle: LAST / Resolution: 3.51→26.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7428 0 0 0 7428
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00975902
X-RAY DIFFRACTIONt_angle_deg1.09103602
X-RAY DIFFRACTIONt_dihedral_angle_d33922
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes1782
X-RAY DIFFRACTIONt_gen_planes10945
X-RAY DIFFRACTIONt_it759020
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.16
X-RAY DIFFRACTIONt_other_torsion2.91
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion10705
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_contact81494
LS refinement shellResolution: 3.51→3.79 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2826 151 5.45 %
Rwork0.2501 2618 -
all0.252 2769 -
obs-2736 98.8 %
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)
10.2416-0.1206-0.7754-0.19420.04970.25790.04420.0306-0.12620.0099-0.0489-0.0072-0.00570.15970.0047-0.04840.0115-0.0330.02960.02150.1515-19.65627.7167-45.722
20.3648-0.10130.0925-0.16150.29090.6417-0.0011-0.0696-0.1447-0.02450.04680.01640.08410.0538-0.04570.33570.0022-0.02640.2010.1245-0.304-57.807615.4465-17.5318
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A32 - 535
2X-RAY DIFFRACTION2{ B|* }B31 - 546

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