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- PDB-4kfs: Structure of the genome packaging NTPase B204 from Sulfolobus tur... -

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Basic information

Entry
Database: PDB / ID: 4kfs
TitleStructure of the genome packaging NTPase B204 from Sulfolobus turreted icosahedral virus 2 in complex with AMP
ComponentsGenome packaging NTPase B204
KeywordsHYDROLASE / FtsK-HerA superfamily / P-loop ATPase / genome packaging NTPase
Function / homology
Function and homology information


nucleotide binding / metal ion binding
Similarity search - Function
P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / CITRATE ANION / Uncharacterized protein
Similarity search - Component
Biological speciesSulfolobus turreted icosahedral virus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.946 Å
AuthorsHapponen, L.J. / Oksanen, E. / Kajander, T. / Goldman, A. / Butcher, S.
CitationJournal: J.Virol. / Year: 2013
Title: The Structure of the NTPase That Powers DNA Packaging into Sulfolobus Turreted Icosahedral Virus 2.
Authors: Happonen, L.J. / Oksanen, E. / Liljeroos, L. / Goldman, A. / Kajander, T. / Butcher, S.J.
History
DepositionApr 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Jul 24, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: Genome packaging NTPase B204
B: Genome packaging NTPase B204
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7519
Polymers49,8162
Non-polymers9367
Water2,306128
1
A: Genome packaging NTPase B204
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4164
Polymers24,9081
Non-polymers5093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Genome packaging NTPase B204
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3355
Polymers24,9081
Non-polymers4274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.600, 61.015, 70.004
Angle α, β, γ (deg.)90.00, 96.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Genome packaging NTPase B204


Mass: 24907.756 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus turreted icosahedral virus 2
Gene: B204, STIV2_B204 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566/pTF16 / References: UniProt: D5IEZ9, Hydrolases

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Non-polymers , 6 types, 135 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 1.98 Å3/Da / Density % sol: 38.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-HCl, 0.2 M magnesium chloride, 30% PEG4000, 5 mM AMP, protein in 50 mM sodium citrate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97372 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 2011
RadiationMonochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97372 Å / Relative weight: 1
ReflectionResolution: 1.946→46.294 Å / Num. all: 28042 / Num. obs: 28041 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.36 % / Biso Wilson estimate: 23.16 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 5.11
Reflection shellResolution: 1.946→2.06 Å / Redundancy: 3.96 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.07 / Num. unique all: 3131 / % possible all: 67.7

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Processing

Software
NameVersionClassification
MxCuBEdata collection
SHARPphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4KFR

4kfr


Resolution: 1.946→46.294 Å / SU ML: 0.56 / σ(F): 1.99 / Phase error: 24.87 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2384 1402 5 %RANDOM
Rwork0.197 ---
obs0.1991 28038 97.44 %-
all-28038 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.594 Å2 / ksol: 0.362 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.7056 Å20 Å22.0218 Å2
2--11.4151 Å20 Å2
3----6.7095 Å2
Refinement stepCycle: LAST / Resolution: 1.946→46.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3214 0 53 128 3395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133360
X-RAY DIFFRACTIONf_angle_d1.1254589
X-RAY DIFFRACTIONf_dihedral_angle_d14.2771190
X-RAY DIFFRACTIONf_chiral_restr0.076510
X-RAY DIFFRACTIONf_plane_restr0.005551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.946-2.01560.28981100.2622097X-RAY DIFFRACTION77
2.0156-2.09630.26361420.2382691X-RAY DIFFRACTION100
2.0963-2.19170.31081430.21142717X-RAY DIFFRACTION100
2.1917-2.30720.2411420.20992691X-RAY DIFFRACTION100
2.3072-2.45180.26961440.19412741X-RAY DIFFRACTION100
2.4518-2.64110.28041420.20332707X-RAY DIFFRACTION100
2.6411-2.90680.25141440.21352726X-RAY DIFFRACTION100
2.9068-3.32730.26561450.19842748X-RAY DIFFRACTION100
3.3273-4.19160.20131440.17552729X-RAY DIFFRACTION100
4.1916-46.3070.19631460.18142789X-RAY DIFFRACTION99

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