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- PDB-4xvn: Crystal structure of the small terminase from thermophilic phage G20C -

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Basic information

Entry
Database: PDB / ID: 4xvn
TitleCrystal structure of the small terminase from thermophilic phage G20C
ComponentsSmall terminase
KeywordsVIRAL PROTEIN / Small terminase / DNA-recognition / Thermophilic phage G20C
Function / homologyDNA binding / Terminase, small subunit
Function and homology information
Biological speciesThermus phage G20c (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsLoredo-Varela, J. / Jenkins, H.T. / Chechik, M. / Greive, S.J. / Antson, A.A.
Funding support United Kingdom, Mexico, 2items
OrganizationGrant numberCountry
Wellcome Trust098230 United Kingdom
Consejo Nacional de Ciencia y Tecnologia de Mexico Mexico
CitationJournal: To Be Published
Title: Crystal structure of the small terminase from thermophilic phage G20C
Authors: Antson, A.A. / Loredo-Varela, J. / Jenkins, H.T. / Chechik, M. / Greive, S.J.
History
DepositionJan 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Small terminase
B: Small terminase
C: Small terminase
D: Small terminase
E: Small terminase
F: Small terminase


Theoretical massNumber of molelcules
Total (without water)116,2706
Polymers116,2706
Non-polymers00
Water00
1
A: Small terminase
B: Small terminase
C: Small terminase

A: Small terminase
B: Small terminase
C: Small terminase

A: Small terminase
B: Small terminase
C: Small terminase


Theoretical massNumber of molelcules
Total (without water)174,4059
Polymers174,4059
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area29490 Å2
ΔGint-222 kcal/mol
Surface area60570 Å2
MethodPISA
2
D: Small terminase
E: Small terminase
F: Small terminase

D: Small terminase
E: Small terminase
F: Small terminase

D: Small terminase
E: Small terminase
F: Small terminase


Theoretical massNumber of molelcules
Total (without water)174,4059
Polymers174,4059
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area33490 Å2
ΔGint-268 kcal/mol
Surface area65200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.585, 152.585, 108.805
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
12A
22B
32C
42D
52E
62F
13A
23B
33C
43D
53E
63F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A5 - 27
2116B5 - 27
3116C5 - 27
4116D5 - 27
5116E5 - 27
6116F5 - 27
1126A35 - 92
2126B35 - 92
3126C35 - 92
4126D35 - 92
5126E35 - 92
6126F35 - 92
1136A104 - 137
2136B104 - 137
3136C104 - 137
4136D104 - 137
5136E104 - 137
6136F104 - 137

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.752048, 0.651563, -0.099442), (-0.658925, 0.739684, -0.136691), (-0.015507, 0.168323, 0.98561)4.45862, 7.18148, -4.34535
3given(0.125544, 0.9796, -0.156913), (-0.973209, 0.090895, -0.211194), (-0.192623, 0.179223, 0.964767)6.73347, 12.38555, -5.77885
4given(-0.647947, -0.758072, -0.074098), (0.761678, -0.644452, -0.067287), (0.003256, -0.100037, 0.994978)-14.38138, 89.730888, 19.03977
5given(-0.066687, -0.995345, -0.06958), (0.997087, -0.063892, -0.041648), (0.037009, -0.072155, 0.996707)41.004181, 79.436859, 20.960239
6given(0.717292, -0.693451, -0.067956), (0.695082, 0.718931, 0.000499), (0.04851, -0.047593, 0.997688)84.92765, 24.78392, 21.36916
7given(1), (1), (1)
8given(0.763812, 0.644839, -0.027834), (-0.645433, 0.763288, -0.028424), (0.002916, 0.039676, 0.999208)0.94644, 1.09867, -0.47871
9given(0.089333, 0.995292, -0.037588), (-0.993491, 0.091722, 0.067542), (0.070671, 0.03131, 0.997008)-0.43356, -3.28953, 1.94806
10given(-0.660869, -0.750306, -0.017117), (0.750446, -0.660924, -0.003026), (-0.009042, -0.014845, 0.999849)-17.60424, 86.422859, 17.19212
11given(-0.030203, -0.999382, -0.018002), (0.999537, -0.030267, 0.003259), (-0.003802, -0.017895, 0.999833)41.60228, 77.621567, 17.85005
12given(0.65929, -0.751728, -0.015549), (0.751626, 0.658372, 0.040065), (-0.019881, -0.038102, 0.999076)82.203957, 26.912661, 18.50053
13given(1), (1), (1)
14given(0.76445, 0.643493, -0.039145), (-0.643581, 0.765284, 0.011992), (0.037674, 0.016026, 0.999162)1.3371, -0.53016, 0.36374
15given(0.185789, 0.98259, 0.00057), (-0.982415, 0.185745, 0.018965), (0.018529, -0.004083, 0.99982)0.0637, -0.68539, 0.15804
16given(-0.695652, -0.718379, 0.000447), (0.717798, -0.695114, -0.039786), (0.028892, -0.027356, 0.999208)-21.40324, 86.911926, 19.472481
17given(-0.058592, -0.998272, -0.004391), (0.998032, -0.058478, -0.022624), (0.022328, -0.005708, 0.999734)39.519939, 79.752502, 18.44894
18given(0.572531, -0.819882, 0.000859), (0.819357, 0.572126, -0.036411), (0.029361, 0.021551, 0.999337)80.328827, 38.83099, 17.54356

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Components

#1: Protein
Small terminase


Mass: 19378.305 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Thermus thermophilus phage G20C / Source: (gene. exp.) Thermus phage G20c (virus) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1L4BKP6*PLUS

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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: 2.1 Å3/Da / Density % sol: 41.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes pH 7.5, 0.4 M ammonium acetate, 18 % (w/v) PEG 3.35 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→45.39 Å / Num. obs: 29032 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 62.4 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 13.8
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.998 / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
SHELXphasing
Aimlessdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→45.39 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.279 / WRfactor Rwork: 0.2487 / FOM work R set: 0.7549 / SU B: 16.595 / SU ML: 0.34 / SU R Cruickshank DPI: 0.9064 / SU Rfree: 0.3416 / Cross valid method: FREE R-VALUE / ESU R: 0.906 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2762 954 3.3 %RANDOM
Rwork0.249 28077 --
obs0.2499 29031 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 146.7 Å2 / Biso mean: 85.772 Å2 / Biso min: 54.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20.36 Å20 Å2
2--0.71 Å20 Å2
3----2.31 Å2
Refine analyzeLuzzati sigma a obs: 0.34 Å
Refinement stepCycle: final / Resolution: 2.6→45.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6209 0 0 0 6209
Num. residues----795
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0196275
X-RAY DIFFRACTIONr_bond_other_d0.0010.026315
X-RAY DIFFRACTIONr_angle_refined_deg0.8572.0128465
X-RAY DIFFRACTIONr_angle_other_deg0.764314464
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1685782
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.63623.916286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.656151082
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5851562
X-RAY DIFFRACTIONr_chiral_restr0.0410.21009
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026966
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021322
X-RAY DIFFRACTIONr_mcbond_it1.438.6163167
X-RAY DIFFRACTIONr_mcbond_other1.438.6163166
X-RAY DIFFRACTIONr_mcangle_it2.5712.9043936
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A359LOOSE POSITIONAL0.585
12B359LOOSE POSITIONAL0.885
13C359LOOSE POSITIONAL0.455
14D359LOOSE POSITIONAL0.485
15E359LOOSE POSITIONAL0.425
16F359LOOSE POSITIONAL0.645
11A359LOOSE THERMAL10.3810
12B359LOOSE THERMAL12.310
13C359LOOSE THERMAL2.8110
14D359LOOSE THERMAL3.5410
15E359LOOSE THERMAL5.110
16F359LOOSE THERMAL5.0110
21A887LOOSE POSITIONAL0.695
22B887LOOSE POSITIONAL0.655
23C887LOOSE POSITIONAL0.915
24D887LOOSE POSITIONAL0.555
25E887LOOSE POSITIONAL0.65
26F887LOOSE POSITIONAL0.615
21A887LOOSE THERMAL14.8710
22B887LOOSE THERMAL8.4410
23C887LOOSE THERMAL11.710
24D887LOOSE THERMAL9.0210
25E887LOOSE THERMAL11.5610
26F887LOOSE THERMAL8.6310
31A426LOOSE POSITIONAL0.55
32B426LOOSE POSITIONAL0.445
33C426LOOSE POSITIONAL0.525
34D426LOOSE POSITIONAL0.585
35E426LOOSE POSITIONAL0.585
36F426LOOSE POSITIONAL0.55
31A426LOOSE THERMAL8.1410
32B426LOOSE THERMAL8.1210
33C426LOOSE THERMAL8.3210
34D426LOOSE THERMAL6.9910
35E426LOOSE THERMAL6.1110
36F426LOOSE THERMAL11.5610
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 70 -
Rwork0.334 2070 -
all-2140 -
obs--99.95 %

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