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- PDB-4r2h: The Crystal Structure of B204, the DNA-packaging ATPase from Sulf... -

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Basic information

Entry
Database: PDB / ID: 4r2h
TitleThe Crystal Structure of B204, the DNA-packaging ATPase from Sulfolobus Turreted Icosahedral Virus
ComponentsSTIV B204 ATPase
KeywordsVIRAL PROTEIN / walker A motif / walker B motif / arginine finger / p-loop ATPase / AAA ATPase / DNA-dependent ATPase
Function / homologyZonular occludens toxin (Zot) / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / metal ion binding / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesSulfolobus turreted icosahedral virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.96 Å
AuthorsDellas, N. / Nicolay, S.J. / Young, M.J.
CitationJournal: J.Virol. / Year: 2015
Title: Structure-Based Mutagenesis of Sulfolobus Turreted Icosahedral Virus B204 Reveals Essential Residues in the Virion-Associated DNA-Packaging ATPase.
Authors: Dellas, N. / Snyder, J.C. / Dills, M. / Nicolay, S.J. / Kerchner, K.M. / Brumfield, S.K. / Lawrence, C.M. / Young, M.J.
History
DepositionAug 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: STIV B204 ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8892
Polymers24,8241
Non-polymers651
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.870, 57.960, 67.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein STIV B204 ATPase


Mass: 24823.814 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus turreted icosahedral virus 1
Gene: B164, B204 / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q6Q0J1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 1-204 CORRESPONDS TO UNP ENTRY Q6Q0J1, HOWEVER ONLY RESIDUES 1-157 IS PRESENT IN Q6Q0J1 AT ...RESIDUES 1-204 CORRESPONDS TO UNP ENTRY Q6Q0J1, HOWEVER ONLY RESIDUES 1-157 IS PRESENT IN Q6Q0J1 AT THE TIME OF PROCESSING THIS ENTRY

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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: 2.1 Å3/Da / Density % sol: 41.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.5M ammonium phosphate dibasic, 0.1M TRIS-HCl pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 2, 2013
Details: Sample to detector distance: 95 to 650 mm. Maximum vertical offset: 60 mm
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.96→43.943 Å / Num. obs: 15207 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 28.7 Å2 / Rsym value: 0.061 / Net I/σ(I): 17.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.96-2.066.30.3152.51391021940.315100
2.06-2.196.40.2173.51322420570.217100
2.19-2.346.40.1475.11246519370.147100
2.34-2.536.40.1126.61172018210.112100
2.53-2.776.40.0828.71080316810.082100
2.77-3.16.40.0611974215220.06100
3.1-3.586.40.05211.6862813570.052100
3.58-4.386.30.03715.4733911660.037100
4.38-6.196.10.0561056579220.056100
6.19-38.6525.60.0317.830685500.0399.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.64 Å38.65 Å
Translation5.64 Å38.65 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHASER2.5.2phasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→38.652 Å / FOM work R set: 0.8471 / SU ML: 0.15 / σ(F): 1.35 / Phase error: 21.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2273 762 5.03 %
Rwork0.1806 --
obs0.1829 15164 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.06 Å2 / Biso mean: 33.74 Å2 / Biso min: 17.17 Å2
Refinement stepCycle: LAST / Resolution: 1.96→38.652 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1684 0 1 89 1774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071726
X-RAY DIFFRACTIONf_angle_d0.9862334
X-RAY DIFFRACTIONf_chiral_restr0.045259
X-RAY DIFFRACTIONf_plane_restr0.005285
X-RAY DIFFRACTIONf_dihedral_angle_d14.361637
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.96-2.11030.23461650.18128262991
2.1103-2.32260.24921500.189428282978
2.3226-2.65860.2521540.211128372991
2.6586-3.34930.26131310.204429053036
3.3493-38.65950.19981620.158130063168

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