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- PDB-3jvo: Crystal structure of bacteriophage HK97 gp6 -

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Basic information

Entry
Database: PDB / ID: 3jvo
TitleCrystal structure of bacteriophage HK97 gp6
ComponentsGp6
KeywordsVIRAL PROTEIN / 13-membered ring
Function / homologyPhage gp6-like head-tail connector protein / Hypothetical protein yqbg / Phage gp6-like head-tail connector protein / Phage gp6-like head-tail connector protein / Orthogonal Bundle / Mainly Alpha / Gp6
Function and homology information
Biological speciesEnterobacteria phage HK97 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsLam, R. / Tuite, A. / Battaile, K.P. / Edwards, A.M. / Maxwell, K.L. / Chirgadze, N.Y.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: The crystal structure of bacteriophage HK97 gp6: defining a large family of head-tail connector proteins.
Authors: Cardarelli, L. / Lam, R. / Tuite, A. / Baker, L.A. / Sadowski, P.D. / Radford, D.R. / Rubinstein, J.L. / Battaile, K.P. / Chirgadze, N. / Maxwell, K.L. / Davidson, A.R.
History
DepositionSep 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gp6
B: Gp6
C: Gp6
D: Gp6
E: Gp6
F: Gp6
G: Gp6
H: Gp6
I: Gp6
J: Gp6
K: Gp6
L: Gp6
M: Gp6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,40622
Polymers164,50813
Non-polymers8989
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34030 Å2
ΔGint-167 kcal/mol
Surface area52520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.751, 200.211, 51.169
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Gp6


Mass: 12654.479 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage HK97 (virus) / Gene: gp6 / Plasmid: modified pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): KM1603 / References: UniProt: Q9MBY2
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 3.06 Å3/Da / Density % sol: 59.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 20% MPD, 0.1M calcium chloride, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 4, 2007 / Details: Si(111) double-crystal monochromator
RadiationMonochromator: Si(111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 115130 / % possible obs: 97.3 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.074 / Χ2: 1.579 / Net I/σ(I): 11.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.185.20.292101930.88187.4
2.18-2.265.50.256106900.97191.6
2.26-2.375.60.215112210.93196
2.37-2.495.90.169115341.01198.5
2.49-2.6560.139117301.1141100
2.65-2.8560.111117741.3011100
2.85-3.1460.084117741.631100
3.14-3.5960.06118671.8741100
3.59-4.525.90.051119742.1241100
4.52-505.60.055123733.606199.3

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Phasing

PhasingMethod: SAD
Phasing MAD set
IDHighest resolution (Å)Lowest resolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_12.140.340010476710195
ANO_12.140.341.08901020650
Phasing MAD set shell
IDResolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_19.17-40.34001087471
ISO_16.57-9.17002086514
ISO_15.39-6.57002773525
ISO_14.68-5.39003271515
ISO_14.19-4.68003799526
ISO_13.83-4.19004197532
ISO_13.55-3.83004588522
ISO_13.32-3.55004949523
ISO_13.13-3.32005257516
ISO_12.97-3.13005586533
ISO_12.83-2.97005853521
ISO_12.71-2.83006171514
ISO_12.61-2.71006487535
ISO_12.51-2.61006686528
ISO_12.43-2.51006879510
ISO_12.35-2.43007058505
ISO_12.28-2.35007153496
ISO_12.22-2.28007116484
ISO_12.16-2.22006990468
ISO_12.1-2.16006781457
ANO_19.17-40.343.65010720
ANO_16.57-9.173.933020770
ANO_15.39-6.573.493027710
ANO_14.68-5.392.919032670
ANO_14.19-4.682.413037970
ANO_13.83-4.192.11041940
ANO_13.55-3.831.806045860
ANO_13.32-3.551.615049470
ANO_13.13-3.321.26052550
ANO_12.97-3.131.067055840
ANO_12.83-2.970.854058520
ANO_12.71-2.830.679061700
ANO_12.61-2.710.579064850
ANO_12.51-2.610.49066840
ANO_12.43-2.510.418068580
ANO_12.35-2.430.355069170
ANO_12.28-2.350.341067510
ANO_12.22-2.280.227065610
ANO_12.16-2.220.302063530
ANO_12.1-2.160.287058840
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
1-101.986-136.003-12.318SE40.771.24
2-141.557-102.541-14.84SE40.81.18
3-109.126-161.273-32.362SE49.41.23
4-112.422-139.353-31.988SE38.651.15
5-145.025-112.259-33.445SE39.611.15
6-93.614-115.872-12.193SE46.321.17
7-125.311-121.549-32.666SE44.271.22
8-119.119-169.548-37.54SE42.411.09
9-155.241-119.359-38.341SE40.711.16
10-120.099-98.323-13.271SE48.191.25
11-99.551-157.898-13.897SE39.031.2
12-124.032-134.877-36.938SE40.091.14
13-93.762-146.947-9.364SE36.751.08
14-128.989-184.746-38.375SE42.371.1
15-140.261-93.917-14.898SE50.981.21
16-150.246-93.123-11.523SE40.111.11
17-117.357-151.638-36.603SE38.31.07
18-132.3-197.042-34.948SE49.081.17
19-132.296-93.348-9.903SE44.411.07
20-137.774-123.394-37.78SE43.91.24
21-91.132-129.06-8.497SE46.041.23
22-163.813-121.371-34.666SE59.831.21
23-86.589-121.849-13.009SE55.521.16
24-146.122-121.147-33.679SE67.971.44
25-115.972-182.023-33.503SE47.521.14
26-118.123-161.195-32.675SE64.611.2
27-172.612-124.106-39.591SE38.631.08
28-80.643-114.589-8.842SE41.831.08
29-87.172-163.816-10.206SE45.881.17
30-124.098-177.9-33.657SE62.261.21
31-130.496-129.066-33.046SE64.621.29
32-186.079-123.742-35.987SE58.71.21
33-92.021-146.868-5.723SE73.561.34
34-93.276-138.198-13.084SE51.841.15
35-123.189-89.76-13.631SE66.241.26
36-90.902-155.874-14.294SE59.421.26
37-120.215-169.178-41.242SE29.840.53
38-127.893-12.773-16.354SE45.831.13
39-78.509-48.49-40.319SE64.541.27
40-34.061-7.183-45.094SE75.961.24
41-51.909-8.814-43.441SE72.261.29
42-9.636-29.764-46.229SE40.710.84
43-170.327-35.397-10.352SE87.251.5
44-115.749-29.605-15.308SE74.521.38
45-175.159-43.565-18.667SE56.610.99
46-109.884-35.825-6.43SE35.580.62
47-140.136-20.118-9.077SE85.371.45
48-157.973-23.313-9.613SE49.870.74
49-67.185-16.568-42.176SE73.841.22
50-59.349-10.939-34.785SE75.681.29
51-123.209-24.734-7.99SE85.941.42
52-18.675-15.342-45.935SE89.751.47
53-111.311-37.475-6.826SE36.130.58
54-156.408-24.869-9.646SE31.680.53
55-7.39-29.501-46.716SE32.040.45
56-113.407-29.231-11.861SE50.440.22
57-47.201-2.803-15.274SE50.440.35
58-83.895-21.983-32.712SE50.970.31
59-7.122-10.791-38.878SE50.970.26
60-82.675-43.326-11.692SE50.970.36
61-168.458-27.089-21.082SE50.970.18
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 114960
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
11.4-10079.90.557830
8.06-11.470.70.8841448
6.58-8.0661.80.9161860
5.7-6.58620.9232146
5.1-5.761.80.9282449
4.66-5.157.20.9372682
4.31-4.6660.60.9492906
4.03-4.3161.90.9483103
3.8-4.0364.30.9473313
3.61-3.864.50.9413456
3.44-3.6165.90.9443618
3.29-3.4467.50.9373826
3.16-3.2967.60.9253935
3.05-3.1669.70.9164086
2.94-3.0572.10.9154278
2.85-2.9473.90.914324
2.77-2.85750.9114570
2.69-2.7775.70.9034573
2.62-2.6977.20.914820
2.55-2.62780.9094834
2.49-2.5578.50.95059
2.43-2.4979.60.9135034
2.38-2.4381.50.9065157
2.33-2.3880.90.9045209
2.28-2.3382.70.8885195
2.24-2.28850.8755180
2.19-2.2485.50.895140
2.16-2.1984.80.8755094
2.1-2.1685.70.8066835

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DM5phasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT3.005data extraction
JDirectordata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→39.78 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.222 / WRfactor Rwork: 0.191 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 8.368 / SU ML: 0.108 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 5763 5 %RANDOM
Rwork0.194 ---
obs0.196 114961 96.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 71.79 Å2 / Biso mean: 36.039 Å2 / Biso min: 19.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10083 0 58 248 10389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02210434
X-RAY DIFFRACTIONr_angle_refined_deg1.2281.9414155
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.80751264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91124.669559
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.32151771
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.391564
X-RAY DIFFRACTIONr_chiral_restr0.0820.21555
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028004
X-RAY DIFFRACTIONr_nbd_refined0.2090.24746
X-RAY DIFFRACTIONr_nbtor_refined0.30.27329
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2375
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.217
X-RAY DIFFRACTIONr_mcbond_it0.9291.56431
X-RAY DIFFRACTIONr_mcangle_it1.414210066
X-RAY DIFFRACTIONr_scbond_it2.27234553
X-RAY DIFFRACTIONr_scangle_it3.6654.54074
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.1580.2823730.2356863861983.954
2.158-2.2170.2723780.237082843388.462
2.217-2.2810.2893670.2357232815493.194
2.281-2.3510.2493870.237259798695.743
2.351-2.4280.2653710.2147191776697.373
2.428-2.5130.2423570.2057036743399.462
2.513-2.6080.2793760.2136837722499.848
2.608-2.7140.2443450.2056677702499.972
2.714-2.8340.2383400.2086344669199.895
2.834-2.9710.222980.26073637399.969
2.971-3.1310.2343040.1975817612399.967
3.131-3.320.2272920.1945481577599.965
3.32-3.5470.1942840.1735183546899.982
3.547-3.8290.2062620.16948525114100
3.829-4.190.1982330.15844974730100
4.19-4.6780.1832140.1624112432999.931
4.678-5.390.1931790.1873603378399.974
5.39-6.5710.281740.22631263300100
6.571-9.1680.2091490.1872454260899.808
9.168-39.7780.22800.2271479161496.592
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.9885-1.9497-0.28532.11310.25660.50850.0829-0.1114-0.4038-0.01490.03360.25370.0706-0.0428-0.1166-0.0457-0.0051-0.0247-0.05360.06050.039211.60718.8394.987
21.556-0.5539-0.26051.83760.53210.49720.0598-0.0968-0.17250.01760.0012-0.070.0366-0.063-0.0609-0.03150.0023-0.00010.01960.0464-0.07023.80835.8875.073
31.35490.03250.15222.34940.65750.450.0113-0.09650.06230.0186-0.0151-0.0007-0.009-0.07930.0038-0.02680.00490.02330.03750.0073-0.11354.86454.685.929
42.14631.97980.35612.67470.42350.48710.0035-0.01160.41620.09260.01410.33740.0311-0.0472-0.0177-0.065400.0433-0.0022-0.01830.003714.57870.8947.354
53.31911.5450.73751.45080.2160.69490.0049-0.05910.32240.0802-0.00840.226-0.0621-0.08390.0036-0.033500.0381-0.0314-0.0284-0.017530.52780.6488.495
62.34050.22890.78571.22350.12610.7688-0.0035-0.03520.02990.10420.01580.0663-0.0642-0.0302-0.01240.0214-0.0097-0.0002-0.0369-0.0183-0.086149.32281.8819.653
72.9055-1.19050.54241.2785-0.41660.6770.0056-0.14130.2450.0509-0.0004-0.0793-0.01130.0093-0.0052-0.0035-0.0167-0.0081-0.0319-0.0475-0.057466.53374.3210.742
81.2759-0.87850.26941.4433-0.3020.6442-0.0064-0.09220.09910.0771-0.01310.0464-0.02720.0840.0196-0.0102-0.0124-0.00570.0158-0.0166-0.087578.10259.68110.984
91.01390.31170.12982.7083-0.36870.35010.0514-0.0831-0.00920.09660.0279-0.0185-0.02270.0803-0.0792-0.0158-0.0177-0.02840.0179-0.0177-0.090781.42741.39910.553
101.66151.6953-0.15853.3226-0.42690.40920.0261-0.0289-0.20170.15270.0348-0.2602-0.00580.0743-0.0609-0.0253-0.0074-0.0627-0.0338-0.0035-0.02476.19823.2959.907
113.18372.3521-0.22572.86790.32690.37270.1175-0.0617-0.31390.2215-0.0203-0.35070.05560.0839-0.09720.01240.0044-0.0874-0.05840.0192-0.025862.9919.9658.683
121.63420.5114-0.36711.2682-0.07090.61250.00640.0048-0.01180.11920.0352-0.07220.05090.0102-0.04160.04460.0051-0.0356-0.05540.0292-0.065345.0024.3757.39
133.0371-0.9205-0.29631.40620.0840.82970.0591-0.0568-0.29140.002-0.01510.20020.0549-0.0757-0.044-0.0164-0.0049-0.0233-0.06190.0503-0.002926.4967.4125.902
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 97
2X-RAY DIFFRACTION2B2 - 97
3X-RAY DIFFRACTION3C1 - 95
4X-RAY DIFFRACTION4D2 - 97
5X-RAY DIFFRACTION5E2 - 97
6X-RAY DIFFRACTION6F2 - 97
7X-RAY DIFFRACTION7G2 - 98
8X-RAY DIFFRACTION8H2 - 97
9X-RAY DIFFRACTION9I2 - 96
10X-RAY DIFFRACTION10J2 - 97
11X-RAY DIFFRACTION11K2 - 97
12X-RAY DIFFRACTION12L2 - 97
13X-RAY DIFFRACTION13M2 - 97

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