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- PDB-1w4c: P4 protein from Bacteriophage PHI12 apo state -

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Basic information

Entry
Database: PDB / ID: 1w4c
TitleP4 protein from Bacteriophage PHI12 apo state
ComponentsNTPASE P4
KeywordsHYDROLASE / DSRNA VIRUS / PACKAGING ATPASE / HEXAMERIC HELICASE / MOLECULAR MOTOR / NON-HYDROLYSABLE ATP ANALOGUE HYDROLASE
Function / homology
Function and homology information


viral genome packaging / ATP 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
Biological speciesBACTERIOPHAGE PHI-12 (bacteriophage)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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
D: NTPASE P4
E: NTPASE P4
F: NTPASE P4
G: NTPASE P4
H: NTPASE P4
I: NTPASE P4
J: NTPASE P4
K: NTPASE P4
L: NTPASE P4
M: NTPASE P4
N: NTPASE P4
O: NTPASE P4
P: NTPASE P4
Q: NTPASE P4
R: NTPASE P4
S: NTPASE P4
T: NTPASE P4
U: NTPASE P4
V: NTPASE P4
W: NTPASE P4
X: NTPASE P4


Theoretical massNumber of molelcules
Total (without water)843,61024
Polymers843,61024
Non-polymers00
Water56,9633162
1
A: NTPASE P4
B: NTPASE P4
C: NTPASE P4
D: NTPASE P4
E: NTPASE P4
F: NTPASE P4


Theoretical massNumber of molelcules
Total (without water)210,9036
Polymers210,9036
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
G: NTPASE P4
H: NTPASE P4
I: NTPASE P4
J: NTPASE P4
K: NTPASE P4
L: NTPASE P4


Theoretical massNumber of molelcules
Total (without water)210,9036
Polymers210,9036
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
M: NTPASE P4
N: NTPASE P4
O: NTPASE P4
P: NTPASE P4
Q: NTPASE P4
R: NTPASE P4


Theoretical massNumber of molelcules
Total (without water)210,9036
Polymers210,9036
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
S: NTPASE P4
T: NTPASE P4
U: NTPASE P4
V: NTPASE P4
W: NTPASE P4
X: NTPASE P4


Theoretical massNumber of molelcules
Total (without water)210,9036
Polymers210,9036
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)115.400, 126.300, 155.600
Angle α, β, γ (deg.)90.00, 91.60, 90.50
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.6393, -0.35965, -0.67967), (-0.09606, 0.83961, -0.53463), (0.76293, 0.40708, 0.50221)107.9213, 59.7056, -52.4323
2given(-0.04792, -0.80733, -0.58816), (-0.55619, 0.51067, -0.65565), (0.82967, 0.29571, -0.4735)188.2156, 129.4904, 25.0874
3given(-0.3688, -0.9144, 0.1669), (-0.91564, 0.32649, -0.23452), (0.15995, -0.23932, -0.95768)163.0288, 139.4172, 154.1659
4given(-0.01227, -0.56279, 0.82651), (-0.80697, 0.49366, 0.32417), (-0.59046, -0.663, -0.46021)58.3525, 75.3392, 206.8051
5given(0.67184, -0.10931, 0.73259), (-0.34562, 0.82851, 0.44059), (-0.65511, -0.5492, 0.51885)-22.1064, 5.4393, 128.4957
6given(-0.02325, 0.76623, 0.64215), (0.77877, -0.38889, 0.49223), (0.62688, 0.51153, -0.58767)-42.42, 27.8273, 29.571
7given(0.35095, 0.93366, -0.07144), (0.93362, -0.35476, -0.05006), (-0.07208, -0.04912, -0.99619)-28.6587, 53.7216, 156.9296
8given(0.0781, 0.62138, -0.77961), (0.60836, -0.64923, -0.45652), (-0.78981, -0.43862, -0.42872)70.1868, 132.4491, 198.6662
9given(-0.59845, 0.16134, -0.78474), (0.11472, -0.95216, -0.28325), (-0.7929, -0.25953, 0.55131)157.7431, 181.3592, 110.6209
10given(-0.99578, 0.00796, -0.09144), (-0.03318, -0.96005, 0.27785), (-0.08558, 0.27971, 0.95626)147.249, 150.8405, -15.5711
11given(-0.72306, 0.30215, 0.62121), (0.30515, -0.66707, 0.67963), (0.61974, 0.68097, 0.39013)49.5377, 71.064, -57.0448
12given(0.39037, 0.91906, -0.05423), (-0.90266, 0.37048, -0.21895), (-0.18114, 0.13442, 0.97423)-90.4263, 194.7163, -74.1331
13given(0.09866, 0.61522, -0.78215), (-0.80211, 0.51436, 0.30341), (0.58897, 0.59744, 0.54422)11.2271, 136.3707, -136.0322
14given(-0.59886, 0.16042, -0.78463), (-0.3476, 0.83057, 0.43512), (0.72149, 0.53331, -0.44163)100.2468, 66.6944, -66.083
15given(-0.99568, 0.00442, -0.09272), (0.00362, 0.99995, 0.00881), (0.09275, 0.00844, -0.99565)90.0407, 59.157, 64.382
16given(-0.71436, 0.29996, 0.63223), (-0.11014, 0.84401, -0.52489), (-0.69105, -0.4446, -0.56989)-9.7845, 120.6941, 127.1724
17given(-0.02392, 0.76003, 0.64944), (-0.56353, 0.52634, -0.63672), (-0.82575, -0.38121, 0.41571)-99.7605, 188.5851, 57.6201
18given(0.67207, -0.11296, 0.73182), (0.13733, -0.95214, -0.27308), (0.72764, 0.28403, -0.62439)-79.3731, 240.453, -30.998
19given(0.99991, -0.01135, -0.00773), (-0.00877, -0.96096, 0.27656), (-0.01057, -0.27647, -0.96096)-56.0241, 210.4511, 93.9246
20given(0.64998, -0.35553, -0.67165), (0.32075, -0.67289, 0.66659), (-0.68894, -0.64871, -0.32333)47.796, 132.5934, 125.7836
21given(-0.05131, -0.80111, -0.59631), (0.77723, -0.40698, 0.47988), (-0.62712, -0.43885, 0.64353)130.9313, 91.863, 31.7414
22given(-0.39024, -0.90822, 0.15114), (0.91337, -0.40257, -0.06082), (0.11608, 0.11431, 0.98664)108.4148, 122.2454, -93.8112
23given(-0.02812, -0.55728, 0.82985), (0.60651, -0.66941, -0.42899), (0.79458, 0.49125, 0.35682)1.2471, 193.8577, -126.7647

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Components

#1: Protein ...
NTPASE P4 / P4 PACKAGING ATPASE


Mass: 35150.430 Da / Num. of mol.: 24
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3162 / 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: 50.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 10% PEG 1500, 100MM SODIUM ACETATE PH 4.8 PROTEIN CONCENTRATION 10 MG/ML, SITTING DROPS, 22C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 8, 2002 / Details: MIRRORS
RadiationMonochromator: DIAMOND(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 291757 / % possible obs: 96 % / Redundancy: 9.7 % / Biso Wilson estimate: 51.632 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.6
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.9 / % possible all: 77

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W44

1w44


Resolution: 2.5→20 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2236 14485 4.8 %RANDOM
Rwork0.2514 ---
obs0.2514 291712 96 %-
Solvent computationSolvent model: MASK / Bsol: 80 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 45.91 Å2
Baniso -1Baniso -2Baniso -3
1-4.866 Å20 Å20 Å2
2--1.822 Å20 Å2
3----6.689 Å2
Refine analyzeLuzzati d res low obs: 20 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms54108 0 0 3162 57270
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_deg1.34
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_it2.8353
X-RAY DIFFRACTIONc_mcangle_it4.4764
X-RAY DIFFRACTIONc_scbond_it4.0724
X-RAY DIFFRACTIONc_scangle_it5.7975
LS refinement shellResolution: 2.5→2.6 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rfree0.3321 1515
Rwork0.3037 28699
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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