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- PDB-6x6o: Crystal structure of T4 protein Spackle as determined by native S... -

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Basic information

Entry
Database: PDB / ID: 6x6o
TitleCrystal structure of T4 protein Spackle as determined by native SAD phasing
ComponentsProtein spackle
KeywordsVIRAL PROTEIN / APOBEC / deaminase / HYDROLASE
Function / homologyProtein spackle / superinfection exclusion / host cell periplasmic space / Protein spackle
Function and homology information
Biological speciesEscherichia virus T4
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.52 Å
AuthorsShi, K. / Kurniawan, F. / Banerjee, S. / Moeller, N.H. / Aihara, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118047 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Crystal structure of bacteriophage T4 Spackle as determined by native SAD phasing.
Authors: Shi, K. / Kurniawan, F. / Banerjee, S. / Moeller, N.H. / Aihara, H.
History
DepositionMay 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein spackle
B: Protein spackle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2936
Polymers24,1522
Non-polymers1424
Water2,468137
1
A: Protein spackle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1824
Polymers12,0761
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein spackle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1112
Polymers12,0761
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.424, 79.822, 93.227
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-203-

CL

21A-344-

HOH

31B-357-

HOH

41B-369-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 23 through 61 or resid 63 through 95))
21(chain B and (resid 23 through 61 or resid 63 through 95))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 23 through 61 or resid 63 through 95))A23 - 61
121(chain A and (resid 23 through 61 or resid 63 through 95))A63 - 95
211(chain B and (resid 23 through 61 or resid 63 through 95))B23 - 61
221(chain B and (resid 23 through 61 or resid 63 through 95))B63 - 95

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Components

#1: Protein Protein spackle


Mass: 12075.799 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia virus T4 / Gene: sp, 61.3 / Production host: Escherichia coli (E. coli) / References: UniProt: P39230
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.71 Å3/Da / Density % sol: 28.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2.5 M ammonium sulfate, 0.05 M sodium acetate buffer, pH 4.5, and 4 % (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.5→60.7 Å / Num. obs: 47113 / % possible obs: 99.9 % / Redundancy: 8.7 % / CC1/2: 1 / Rmerge(I) obs: 0.033 / Net I/σ(I): 29.7
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 9 % / Rmerge(I) obs: 1.471 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1310 / CC1/2: 0.647 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
PDB_EXTRACT3.25data extraction
XDSdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.52→40.104 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1907 2299 4.88 %
Rwork0.1733 44813 -
obs0.1742 47112 95.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.51 Å2 / Biso mean: 42.881 Å2 / Biso min: 21.76 Å2
Refinement stepCycle: final / Resolution: 1.52→40.104 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 0 4 138 1354
Biso mean--84.51 45.25 -
Num. residues----150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091236
X-RAY DIFFRACTIONf_angle_d0.9981663
X-RAY DIFFRACTIONf_dihedral_angle_d17.316773
X-RAY DIFFRACTIONf_chiral_restr0.057181
X-RAY DIFFRACTIONf_plane_restr0.007219
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A692X-RAY DIFFRACTION10.127TORSIONAL
12B692X-RAY DIFFRACTION10.127TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.52-1.55310.3681450.3626279695
1.5531-1.58920.29921150.3353277494
1.5892-1.62890.35641450.3139281696
1.6289-1.6730.37571490.3094281196
1.673-1.72220.32131470.2916279096
1.7222-1.77780.30191600.284273594
1.7778-1.84130.28551360.2373273594
1.8413-1.9150.22161680.2142285197
1.915-2.00220.24171380.2028279497
2.0022-2.10780.20471510.1812288596
2.1078-2.23980.20731570.1604276496
2.2398-2.41270.21261330.1619280295
2.4127-2.65550.18911290.1543274294
2.6555-3.03960.17241240.1638292598
3.0396-3.82910.16271310.1501285097
3.8291-40.1040.14821710.1516274394
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.1609-4.5833-5.69135.21665.67619.1963-0.23580.0290.15040.24380.1222-0.2332-0.1015-0.22820.22460.18330.0072-0.04040.34060.00830.306118.7519.37416.824
27.8726-5.4265-1.60364.20182.01623.433-0.2701-0.37760.41320.48110.2085-0.52910.0046-0.11750.06180.2640.0379-0.07060.425-0.02620.318727.324.30726.099
33.50523.09472.32753.14380.79955.16320.30010.2033-0.2828-0.1143-0.0899-0.77210.32520.8062-0.29320.28450.0651-0.05950.5428-0.02050.441338.8552.80828.822
44.02841.31533.34483.10490.9865.4862-0.1041-0.22010.41290.308-0.0943-0.3989-0.13890.08980.11590.21770.0065-0.06150.3792-0.01840.443429.3729.87318.633
53.03230.6262-2.81573.0953-0.73213.65880.37741.1160.0407-0.603-0.7826-0.4907-0.04690.36950.37780.22640.0385-0.00440.4328-0.01040.308729.0223.25210.141
66.87746.30845.37248.28234.02024.5553-0.2690.13330.4052-0.14790.6663-1.1673-0.2861.0422-0.34120.20620.0091-0.03730.5063-0.10150.444836.4911.88918.634
76.2613-3.5026-3.53942.74313.85198.90810.06260.10860.3497-0.05420.117-0.37530.08420.285-0.1950.1928-0.00540.02470.3790.01380.36248.76723.34537.556
81.0417-1.3075-0.65683.692.15812.13890.00690.0292-0.15980.0097-0.0290.07420.2954-0.2060.05720.1642-0.0044-0.02830.3761-0.01270.294439.75414.11841.77
93.73621.2712-1.68112.5254-0.26232.40720.11990.0767-0.15980.0477-0.10970.6450.4304-1.1764-0.06390.2737-0.0768-0.01520.5965-0.03290.517928.29711.18241.902
102.08180.80210.80038.75014.08775.38050.1850.2876-0.0458-0.1543-0.10490.0820.1396-0.1644-0.04280.15710.0068-0.01030.3930.01870.310237.96821.70236.209
114.8568-5.07470.21977.26881.70723.07870.33940.23330.7842-0.03440.1705-0.051-0.5104-0.5561-0.42880.20860.00630.03430.35450.00050.3637.93330.00942.98
122.2751-0.51230.79970.2625-0.72392.4003-0.06970.08860.14120.0265-0.04981.1689-0.1495-0.8305-0.14510.19390.03880.00670.5588-0.02830.620727.33121.87943.407
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 23:36 )A23 - 36
2X-RAY DIFFRACTION2( CHAIN A AND RESID 37:55 )A37 - 55
3X-RAY DIFFRACTION3( CHAIN A AND RESID 56:70 )A56 - 70
4X-RAY DIFFRACTION4( CHAIN A AND RESID 71:80 )A71 - 80
5X-RAY DIFFRACTION5( CHAIN A AND RESID 81:86 )A81 - 86
6X-RAY DIFFRACTION6( CHAIN A AND RESID 87:95 )A87 - 95
7X-RAY DIFFRACTION7( CHAIN B AND RESID 23:36 )B23 - 36
8X-RAY DIFFRACTION8( CHAIN B AND RESID 37:55 )B37 - 55
9X-RAY DIFFRACTION9( CHAIN B AND RESID 56:70 )B56 - 70
10X-RAY DIFFRACTION10( CHAIN B AND RESID 71:80 )B71 - 80
11X-RAY DIFFRACTION11( CHAIN B AND RESID 81:86 )B81 - 86
12X-RAY DIFFRACTION12( CHAIN B AND RESID 87:98 )B87 - 98

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