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- PDB-1w44: P4 protein from Bacteriophage PHI12 in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 1w44
TitleP4 protein from Bacteriophage PHI12 in complex with ADP
ComponentsNTPASE P4
KeywordsHYDROLASE / VIRUS DSRNA / 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
ADENOSINE-5'-DIPHOSPHATE / NTPase P4
Similarity search - Component
Biological speciesBACTERIOPHAGE PHI-12 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 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 1.1May 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 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.5May 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

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)106,7336
Polymers105,4513
Non-polymers1,2823
Water13,944774
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)213,46612
Polymers210,9036
Non-polymers2,5636
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area27680 Å2
ΔGint-102.8 kcal/mol
Surface area63080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.185, 130.908, 158.831
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(0.5015, -0.00213, -0.86516), (0.01245, 0.99991, 0.00476), (0.86507, -0.01316, 0.50148)26.22544, -1.02493, -44.98109
2given(-0.4985, 0.00403, -0.86688), (0.00964, 0.99995, -0.00089), (0.86684, -0.0088, -0.49851)78.57649, -0.74916, -45.27072

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Components

#1: Protein NTPASE P4 / P4 PACKAGING ATPASE FROM BACTERIOPHAGE PHI12


Mass: 35150.430 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTERIOPHAGE PHI-12 (virus) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 774 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 10% PEG 1500, 100MM SODIUM ACETATE PH 4.8 10MM ADP, PROTEIN CONCENTRATION 10 MG/ML, SITTING DROP, 22C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 24, 2002 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 68669 / % possible obs: 93 % / Redundancy: 24 % / Biso Wilson estimate: 39.1 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 32
Reflection shellResolution: 2→20 Å / Redundancy: 15 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.4 / % possible all: 97

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→20 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2277 3482 4.7 %RANDOM
Rwork0.1823 ---
obs0.1823 68395 92.4 %-
Solvent computationSolvent model: MASK / Bsol: 80 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 44.5 Å2
Baniso -1Baniso -2Baniso -3
1-6.641 Å20 Å20 Å2
2---12.715 Å20 Å2
3---6.074 Å2
Refine analyzeLuzzati d res low obs: 20 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6867 0 81 774 7722
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
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_deg1.58
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_it3.9224
X-RAY DIFFRACTIONc_mcangle_it5.18216
X-RAY DIFFRACTIONc_scbond_it6.2226
X-RAY DIFFRACTIONc_scangle_it8.3768
LS refinement shellResolution: 2→2.09 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rfree0.3392 443
Rwork0.2917 8441
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2ADP_2.PAR
X-RAY DIFFRACTION3WATER_REP.PARAM

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