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- PDB-1w47: P4 protein from Bacteriophage PHI12 in complex with ADP and MN -

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Basic information

Entry
Database: PDB / ID: 1w47
TitleP4 protein from Bacteriophage PHI12 in complex with ADP and MN
ComponentsNTPASE P4
KeywordsHYDROLASE / DSRNA VIRUS / PACKAGING ATPASE / HEXAMERIC HELICASE / MOLECULAR MOTOR / NON-HYDROLYSABLE ATP ANALOGUE
Function / homology
Function and homology information


viral genome packaging / ATP binding / metal ion binding
Similarity search - Function
duf1285 protein fold - #20 / duf1285 protein fold / Packaging enzyme P4 / ATPase P4 of dsRNA bacteriophage phi-12 / P-loop containing nucleotide triphosphate hydrolases / Roll / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / NTPase P4
Similarity search - Component
Biological speciesBACTERIOPHAGE PHI-12 (bacteriophage)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.5 Å
AuthorsMancini, E.J. / Kainov, D.E. / Grimes, J.M. / Tuma, R. / Bamford, D.H. / Stuart, D.I.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2004
Title: Atomic Snapshots of an RNA Packaging Motor Reveal Conformational Changes Linking ATP Hydrolysis to RNA Translocation
Authors: Mancini, E.J. / Kainov, D.E. / Grimes, J.M. / Tuma, R. / Bamford, D.H. / Stuart, D.I.
History
DepositionJul 22, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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 / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_id / _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: NTPASE P4
B: NTPASE P4
C: NTPASE P4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,8989
Polymers105,4513
Non-polymers1,4466
Water9,008500
1
A: NTPASE P4
B: NTPASE P4
C: NTPASE P4
hetero molecules

A: NTPASE P4
B: NTPASE P4
C: NTPASE P4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,79518
Polymers210,9036
Non-polymers2,89312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)104.800, 128.200, 158.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.49825, 0.00304, -0.86703), (0.00406, 0.99997, 0.00584), (0.86702, -0.00643, 0.49823)26.23811, -0.37084, -45.128
2given(-0.4987, 0.00339, -0.86677), (0.00937, 0.99995, -0.00149), (0.86672, -0.00887, -0.49871)78.37495, -0.69053, -45.09346

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Components

#1: Protein NTPASE P4 / P4 PACKAGING ATPASE


Mass: 35150.430 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTERIOPHAGE PHI-12 (bacteriophage) / Plasmid: PPG27 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q94M05
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 500 / 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: 2.5 Å3/Da / Density % sol: 48.2 %
Description: CO-CRYSTALS OF P4-ADP-MN ARE ISOMORPHOUS TO P4-ADP CRYSTALS
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 10% PEG 1500, 100MM SODIUM ACETATE PH 4.8 10 MM ADP 10MM MNCL, PROTEIN CONCENTRATION 10 MG/ML, SITTING DROPS, 22C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.74363
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 10, 2003 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.74363 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 36738 / % possible obs: 100 % / Redundancy: 12.2 % / Biso Wilson estimate: 50.316 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 31.3
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 7 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 5.3 / % possible all: 96

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.5→30 Å / Data cutoff high absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1985 3509 4.9 %RANDOM
Rwork0.2392 ---
obs0.2392 33382 98.6 %-
Solvent computationSolvent model: MASK / Bsol: 80 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 42.759 Å2
Baniso -1Baniso -2Baniso -3
1-6.006 Å20 Å20 Å2
2---14.216 Å20 Å2
3---8.113 Å2
Refine analyzeLuzzati d res low obs: 30 Å
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6510 0 84 500 7094
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.1574
X-RAY DIFFRACTIONc_mcangle_it6.126
X-RAY DIFFRACTIONc_scbond_it6.8336
X-RAY DIFFRACTIONc_scangle_it8.8748
LS refinement shellResolution: 2.5→2.6 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rfree0.2379 195
Rwork0.2657 3905
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ADP_2.PARADP_2.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP

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