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- PDB-2vhq: P4 PROTEIN FROM BACTERIOPHAGE PHI12 S252A mutant in complex with ... -

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Basic information

Entry
Database: PDB / ID: 2vhq
TitleP4 PROTEIN FROM BACTERIOPHAGE PHI12 S252A mutant in complex with ATP AND MG
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'-TRIPHOSPHATE / NTPase P4
Similarity search - Component
Biological speciesPSEUDOMONAS PHAGE PHI12 (bacteriophage)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.15 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 22, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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_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 / _pdbx_struct_conn_angle.value / _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
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)106,9989
Polymers105,4033
Non-polymers1,5946
Water10,629590
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)213,99518
Polymers210,8076
Non-polymers3,18912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area29700 Å2
ΔGint-89.2 kcal/mol
Surface area79420 Å2
MethodPQS
Unit cell
Length a, b, c (Å)105.244, 129.387, 158.978
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

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 701
2114B1 - 701
3114C1 - 701

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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-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 590 / 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: 2.6 Å3/Da / Density % sol: 52 %
Description: CRYSTALS OF P4 MUTANT S252A IN COMPLEX WITH ATP AND MG ARE ISOMORPOUS WITH P4-AMPCPP-MG CRYSTALS
Crystal growpH: 4.8 / Details: 10% PEG 1500, 100MM NAAC PH 4.8, 5MM ATP, 5MM MGCL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.072
DetectorType: ADSC CCD / Detector: CCD / Date: May 16, 2006 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 98926 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 15
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

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

Resolution: 2.15→100.5 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.918 / SU B: 4.85 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2994 5.1 %RANDOM
Rwork0.195 ---
obs0.198 56185 99.9 %-
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: 35.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å20 Å20 Å2
2--1.64 Å20 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 2.15→100.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6849 0 96 590 7535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0217070
X-RAY DIFFRACTIONr_bond_other_d0.0010.024590
X-RAY DIFFRACTIONr_angle_refined_deg1.3111.9619595
X-RAY DIFFRACTIONr_angle_other_deg0.934311223
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8715899
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.23324.329298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.572151168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8591539
X-RAY DIFFRACTIONr_chiral_restr0.1210.21114
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027868
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021398
X-RAY DIFFRACTIONr_nbd_refined0.2070.21393
X-RAY DIFFRACTIONr_nbd_other0.2010.24609
X-RAY DIFFRACTIONr_nbtor_refined0.1730.23364
X-RAY DIFFRACTIONr_nbtor_other0.0830.23871
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2541
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.230.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2711.55768
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.38727149
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.69432993
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4824.52445
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

Ens-ID: 1 / Number: 3822 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.390.5
2Bmedium positional0.370.5
3Cmedium positional0.420.5
1Amedium thermal0.632
2Bmedium thermal0.572
3Cmedium thermal0.712
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.307 216
Rwork0.211 4120

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