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- PDB-1w48: P4 protein from Bacteriophage PHI12 in complex with AMPcPP -

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Basic information

Entry
Database: PDB / ID: 1w48
TitleP4 protein from Bacteriophage PHI12 in complex with AMPcPP
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 / Roll / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / NTPase P4
Similarity search - Component
Biological speciesPSEUDOMONAS PHAGE PHI12 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.3 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 1.0Oct 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2May 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 1.3May 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 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)106,9676
Polymers105,4513
Non-polymers1,5163
Water14,250791
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)213,93412
Polymers210,9036
Non-polymers3,0316
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area28400 Å2
ΔGint-91.8 kcal/mol
Surface area63030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.637, 132.083, 159.291
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(0.49732, 0.00198, -0.86756), (0.00404, 0.99998, 0.0046), (0.86756, -0.0058, 0.4973)26.62063, -0.45453, -45.51785
2given(-0.50135, 0.00514, -0.86523), (0.00184, 0.99999, 0.00488), (0.86524, 0.00086, -0.50135)79.22157, -0.16455, -45.63655

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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.) PSEUDOMONAS PHAGE PHI12 (virus) / Plasmid: PPG27 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q94M05
#2: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 791 / 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-AMPCPP ARE ISOMORPHOUS WITH 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 10MM AMPCPP, PROTEIN CONCENTRATION 10 MG/ML, SITTING DROPS, 22C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97564
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 23, 2004 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97564 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 46820 / % possible obs: 95 % / Redundancy: 7.7 % / Biso Wilson estimate: 33.434 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 22.4
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 9 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 3.9 / % possible all: 98

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.3→20 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2175 2332 4.7 %RANDOM
Rwork0.1638 ---
obs0.1638 46905 94.4 %-
Solvent computationSolvent model: MASK / Bsol: 80 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 38.599 Å2
Baniso -1Baniso -2Baniso -3
1-10.097 Å20 Å20 Å2
2---15.714 Å20 Å2
3---5.616 Å2
Refine analyzeLuzzati d res low obs: 20 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6867 0 93 791 7751
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.8
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_it4.2044
X-RAY DIFFRACTIONc_mcangle_it5.4186
X-RAY DIFFRACTIONc_scbond_it7.3586
X-RAY DIFFRACTIONc_scangle_it9.4998
LS refinement shellResolution: 2.3→2.4 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rfree0.2553 276
Rwork0.2201 5571
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2APC_XPLOR_PAR2.TXTAPC_XPLOR_TOP2.TXT
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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