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- PDB-2vhj: P4 PROTEIN FROM BACTERIOPHAGE PHI12 S252A mutant in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 2vhj
TitleP4 PROTEIN FROM BACTERIOPHAGE PHI12 S252A mutant in complex with ADP
ComponentsNTPASE P4
KeywordsHYDROLASE / NON- HYDROLYSABLE ATP ANALOGUE / VIRUS DSRNA / MOLECULAR MOTOR / PACKAGING ATPASE / HEXAMERIC HELICASE
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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / NTPase P4
Similarity search - Component
Biological speciesPSEUDOMONAS PHAGE PHI12 (bacteriophage)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.8 Å
AuthorsKainov, D.E. / Mancini, E.J. / Telenius, J. / Lisal, J. / Grimes, J.M. / Bamford, D.H. / Stuart, D.I. / Tuma, R.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural Basis of Mechanochemical Coupling in a Hexameric Molecular Motor.
Authors: Kainov, D.E. / Mancini, E.J. / Telenius, J. / Lisal, J. / Grimes, J.M. / Bamford, D.H. / Stuart, D.I. / Tuma, R.
History
DepositionNov 21, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)106,6856
Polymers105,4033
Non-polymers1,2823
Water16,123895
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)213,37012
Polymers210,8076
Non-polymers2,5636
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area26270 Å2
ΔGint-74.8 kcal/mol
Surface area78730 Å2
MethodPQS
Unit cell
Length a, b, c (Å)104.940, 128.852, 158.266
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B
32C

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETSERSER6AA1 - 2991 - 299
21METMETSERSER6BB1 - 2991 - 299
31METMETSERSER6CC1 - 2991 - 299
12ADPADPADPADP1AD1301
22ADPADPADPADP1BE1301
32ADPADPADPADP1CF1301

NCS ensembles :
ID
1
2

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Components

#1: Protein NTPASE P4 / P4


Mass: 35134.430 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PHAGE PHI12 (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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 895 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 252 TO ALA ENGINEERED RESIDUE IN CHAIN B, SER 252 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, SER 252 TO ALA ENGINEERED RESIDUE IN CHAIN B, SER 252 TO ALA ENGINEERED RESIDUE IN CHAIN C, SER 252 TO ALA
Sequence detailsPOINT MUTATION INTRODUCED AT S252 INTO A252 WHEN COMPARED TO UNIPROT Q94M05

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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: 52 %
Description: CRYSTALS OF P4 MUTANT S252A IN COMPLEX WITH ADP ARE ISOMORPHOUS WITH P4-ADP-MG CRYSTALS
Crystal growpH: 4.8 / Details: 10% PEG 1500, 100MM NAAC PH 4.8, 5MM ADP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 5, 2004 / Details: MIRRORS
RadiationMonochromator: DIAMOND (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 98926 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 28
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.8 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.8→100 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.53 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.237 4940 5 %RANDOM
Rwork0.2 ---
obs0.202 93889 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å20 Å2
2--2.02 Å20 Å2
3----1.1 Å2
Refinement stepCycle: LAST / Resolution: 1.8→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6510 0 81 895 7486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0216734
X-RAY DIFFRACTIONr_bond_other_d0.0010.024364
X-RAY DIFFRACTIONr_angle_refined_deg1.2011.9589145
X-RAY DIFFRACTIONr_angle_other_deg0.85310666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9295862
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.20224.199281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.592151094
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5021536
X-RAY DIFFRACTIONr_chiral_restr0.1290.21055
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027557
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021350
X-RAY DIFFRACTIONr_nbd_refined0.2030.21390
X-RAY DIFFRACTIONr_nbd_other0.2020.24531
X-RAY DIFFRACTIONr_nbtor_refined0.1730.23290
X-RAY DIFFRACTIONr_nbtor_other0.0830.23533
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2745
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.237
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2680.281
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.247
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0041.55527
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.12526832
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.50432869
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.154.52313
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
21A37tight positional0.010.05
22B37tight positional0.010.05
23C37tight positional0.010.05
11A3574loose positional0.335
12B3574loose positional0.375
13C3574loose positional0.425
21A37tight thermal0.010.5
22B37tight thermal0.010.5
23C37tight thermal0.010.5
11A3574loose thermal1.3610
12B3574loose thermal1.0710
13C3574loose thermal1.5810
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.309 368
Rwork0.261 6726

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