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

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Basic information

Entry
Database: PDB / ID: 4kft
TitleStructure of the genome packaging NTPase B204 from Sulfolobus turreted icosahedral virus 2 in complex with ATP-gammaS
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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / CITRATE ANION / Uncharacterized protein
Similarity search - Component
Biological speciesSulfolobus turreted icosahedral virus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.241 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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
C: Genome packaging NTPase B204
D: Genome packaging NTPase B204
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,92326
Polymers99,6314
Non-polymers4,29222
Water3,981221
1
A: Genome packaging NTPase B204
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0145
Polymers24,9081
Non-polymers1,1064
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Genome packaging NTPase B204
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,50610
Polymers24,9081
Non-polymers1,5989
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Genome packaging NTPase B204
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5214
Polymers24,9081
Non-polymers6133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Genome packaging NTPase B204
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8827
Polymers24,9081
Non-polymers9746
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.726, 65.185, 71.620
Angle α, β, γ (deg.)90.55, 93.65, 91.59
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Genome packaging NTPase B204


Mass: 24907.756 Da / Num. of mol.: 4
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, 243 molecules

#2: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.18 Å3/Da / Density % sol: 43.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.1 M Tris-HCl, 0.2 M magnesium chloride, 30% PEG8000, 5 mM ATPyS, protein in 50 mM sodium citrate, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 27, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.24→46.613 Å / Num. all: 39248 / Num. obs: 39248 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.39 % / Biso Wilson estimate: 31.97 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 10.82
Reflection shellResolution: 2.24→2.38 Å / Redundancy: 3.37 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 2.09 / Num. unique all: 5963 / % possible all: 91.3

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Processing

Software
NameVersionClassification
MxCuBEdata collection
SHARPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4KFR

4kfr


Resolution: 2.241→46.613 Å / SU ML: 0.32 / σ(F): 1.99 / Phase error: 28.2 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2465 1963 5 %RANDOM
Rwork0.1811 ---
obs0.1844 39238 96.93 %-
all-39238 --
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.241→46.613 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6272 0 214 221 6707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136699
X-RAY DIFFRACTIONf_angle_d1.2059185
X-RAY DIFFRACTIONf_dihedral_angle_d15.4442339
X-RAY DIFFRACTIONf_chiral_restr0.0821036
X-RAY DIFFRACTIONf_plane_restr0.0051082
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.241-2.29680.35241210.26332296X-RAY DIFFRACTION85
2.2968-2.35880.31911410.23442686X-RAY DIFFRACTION97
2.3588-2.42830.29081420.22162691X-RAY DIFFRACTION97
2.4283-2.50660.31791400.22382664X-RAY DIFFRACTION98
2.5066-2.59620.30261430.21062717X-RAY DIFFRACTION97
2.5962-2.70010.33431400.20972652X-RAY DIFFRACTION98
2.7001-2.8230.30011410.21732688X-RAY DIFFRACTION98
2.823-2.97180.34221420.2252699X-RAY DIFFRACTION98
2.9718-3.1580.2791420.21062684X-RAY DIFFRACTION98
3.158-3.40180.25951420.18082710X-RAY DIFFRACTION98
3.4018-3.7440.2451410.16222672X-RAY DIFFRACTION98
3.744-4.28540.17971430.14742712X-RAY DIFFRACTION98
4.2854-5.39790.18491420.13232706X-RAY DIFFRACTION98
5.3979-46.62260.1931430.16772698X-RAY DIFFRACTION98

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