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

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Basic information

Entry
Database: PDB / ID: 4kfu
TitleStructure of the genome packaging NTPase B204 from Sulfolobus turreted icosahedral virus 2 in complex with AMPPCP
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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / CITRATE ANION / Uncharacterized protein
Similarity search - Component
Biological speciesSulfolobus turreted icosahedral virus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.892 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
C: Genome packaging NTPase B204
D: Genome packaging NTPase B204
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,69522
Polymers99,6314
Non-polymers4,06418
Water7,710428
1
A: Genome packaging NTPase B204
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4359
Polymers24,9081
Non-polymers1,5278
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Genome packaging NTPase B204
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4359
Polymers24,9081
Non-polymers1,5278
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Genome packaging NTPase B204
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4132
Polymers24,9081
Non-polymers5051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Genome packaging NTPase B204
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4132
Polymers24,9081
Non-polymers5051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.558, 65.227, 72.118
Angle α, β, γ (deg.)90.85, 93.77, 91.56
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 , 5 types, 446 molecules

#2: Chemical
ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-FLC / CITRATE ANION


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


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.19 Å3/Da / Density % sol: 43.9 %
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 AMPPCP, 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: 1.89→48.717 Å / Num. all: 65868 / Num. obs: 65868 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.94 % / Biso Wilson estimate: 32.05 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 11.78
Reflection shellResolution: 1.89→2.01 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.708 / Mean I/σ(I) obs: 1.94 / Num. unique all: 10093 / % possible all: 92.4

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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: 1.892→48.717 Å / SU ML: 0.5 / σ(F): 1.99 / Phase error: 25.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2336 3296 5.01 %RANDOM
Rwork0.1883 ---
obs0.1906 65852 97.41 %-
all-65852 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.506 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.6749 Å20.0473 Å22.8092 Å2
2--8.9918 Å2-1.2774 Å2
3----5.3169 Å2
Refinement stepCycle: LAST / Resolution: 1.892→48.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6352 0 214 428 6994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116766
X-RAY DIFFRACTIONf_angle_d1.149233
X-RAY DIFFRACTIONf_dihedral_angle_d16.5042415
X-RAY DIFFRACTIONf_chiral_restr0.0781031
X-RAY DIFFRACTIONf_plane_restr0.0051101
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.892-1.91860.30371130.28132093X-RAY DIFFRACTION78
1.9186-1.94720.31111340.23892580X-RAY DIFFRACTION97
1.9472-1.97760.26281390.23282622X-RAY DIFFRACTION97
1.9776-2.010.2871370.22882613X-RAY DIFFRACTION98
2.01-2.04470.30271370.23262625X-RAY DIFFRACTION97
2.0447-2.08190.32131370.22832592X-RAY DIFFRACTION97
2.0819-2.12190.26841400.22122646X-RAY DIFFRACTION98
2.1219-2.16520.28231350.21032545X-RAY DIFFRACTION98
2.1652-2.21230.27511400.1982670X-RAY DIFFRACTION98
2.2123-2.26380.23821380.18882594X-RAY DIFFRACTION98
2.2638-2.32040.20361410.18782665X-RAY DIFFRACTION98
2.3204-2.38310.25041360.1882614X-RAY DIFFRACTION98
2.3831-2.45330.27161370.19342619X-RAY DIFFRACTION98
2.4533-2.53240.27761390.20472621X-RAY DIFFRACTION98
2.5324-2.62290.27221380.20332639X-RAY DIFFRACTION98
2.6229-2.7280.27471400.20642661X-RAY DIFFRACTION99
2.728-2.85210.24921380.19822595X-RAY DIFFRACTION98
2.8521-3.00240.2431410.19492649X-RAY DIFFRACTION99
3.0024-3.19050.23671370.1922627X-RAY DIFFRACTION99
3.1905-3.43680.21641410.17682690X-RAY DIFFRACTION99
3.4368-3.78250.20781390.16142637X-RAY DIFFRACTION99
3.7825-4.32960.1741410.15212649X-RAY DIFFRACTION99
4.3296-5.45370.16681390.14982672X-RAY DIFFRACTION99
5.4537-48.73340.22591390.19772638X-RAY DIFFRACTION99

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