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- PDB-4r2i: The Crystal Structure of STIV B204 complexed with AMP-PNP -

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Basic information

Entry
Database: PDB / ID: 4r2i
TitleThe Crystal Structure of STIV B204 complexed with AMP-PNP
ComponentsSTIV B204 ATPase
KeywordsVIRAL PROTEIN / P-loop / Arginine finger / ATP binding / DNA-dependent ATPase / walker A motif / walker B motif / p-loop ATPase / AAA 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 / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Uncharacterized protein
Function and homology information
Biological speciesSulfolobus turreted icosahedral virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 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)25,3953
Polymers24,8241
Non-polymers5722
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.360, 58.320, 67.320
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*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.07 Å3/Da / Density % sol: 40.59 %
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: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 16, 2013
Details: Shutterless data collection; Fine phi slicing experiments
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.05→44.08 Å / Num. obs: 13092 / % possible obs: 97.5 % / Redundancy: 3.4 % / Rsym value: 0.073 / Net I/σ(I): 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.05-2.163.50.4261.7666319170.42699.3
2.16-2.293.30.2712.7593417940.27198.1
2.29-2.453.30.2023.7545816430.20296
2.45-2.653.50.1534.9559315790.15398.5
2.65-2.93.40.1086.4492714600.10898.9
2.9-3.243.30.0749.7427912890.07495.6
3.24-3.743.50.05113.1421111920.05198.7
3.74-4.583.20.03916.631029690.03995.1
4.58-6.483.50.03717.128288020.03798
6.48-44.083.10.03115.314064470.03192.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.42 Å38.91 Å
Translation5.42 Å38.91 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
PHASER2.5.5phasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→44.08 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.779 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.236 644 4.9 %RANDOM
Rwork0.1829 ---
obs0.1855 13056 96.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.04 Å2 / Biso mean: 31.137 Å2 / Biso min: 15.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.22 Å2-0 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.05→44.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1722 0 32 59 1813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191801
X-RAY DIFFRACTIONr_bond_other_d0.0010.021732
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.9642443
X-RAY DIFFRACTIONr_angle_other_deg0.84233980
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9175206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.97323.33381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.24515322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.788158
X-RAY DIFFRACTIONr_chiral_restr0.1060.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021950
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02429
X-RAY DIFFRACTIONr_mcbond_it2.5952.772827
X-RAY DIFFRACTIONr_mcbond_other2.5962.77826
X-RAY DIFFRACTIONr_mcangle_it3.6384.1461032
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 59 -
Rwork0.227 918 -
all-977 -
obs--99.09 %

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