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- PDB-4zws: Crystal Structure of the Bacteriophage T4 recombination mediator ... -

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Basic information

Entry
Database: PDB / ID: 4zws
TitleCrystal Structure of the Bacteriophage T4 recombination mediator protein UvsY, Lattice Type III
ComponentsRecombination protein uvsYGenetic recombination
KeywordsVIRAL PROTEIN / recombination / DNA binding / homo-heptamer / asymmetry / alpha barrel
Function / homologyRecombination, repair and ssDNA binding protein UvsY / Recombination, repair and ssDNA binding protein UvsY / DNA biosynthetic process / DNA recombination / DNA binding / Recombination protein uvsY
Function and homology information
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGajewski, S. / White, S.W.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM066934 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA21765 United States
American Lebanese-Syrian Associated Charities (ALSAC) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structure and mechanism of the phage T4 recombination mediator protein UvsY.
Authors: Gajewski, S. / Waddell, M.B. / Vaithiyalingam, S. / Nourse, A. / Li, Z. / Woetzel, N. / Alexander, N. / Meiler, J. / White, S.W.
History
DepositionMay 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Apr 20, 2016Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Recombination protein uvsY
B: Recombination protein uvsY
C: Recombination protein uvsY
D: Recombination protein uvsY
E: Recombination protein uvsY
F: Recombination protein uvsY
G: Recombination protein uvsY


Theoretical massNumber of molelcules
Total (without water)111,0577
Polymers111,0577
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15120 Å2
ΔGint-117 kcal/mol
Surface area35880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.571, 123.571, 332.465
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F
71chain G

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1METMETGLYGLYchain AAA1 - 1361 - 136
2METMETGLYGLYchain BBB1 - 1361 - 136
3METMETALAALAchain CCC1 - 1351 - 135
4ARGARGGLYGLYchain DDD2 - 1362 - 136
5METMETALAALAchain EEE1 - 1351 - 135
6METMETALAALAchain FFF1 - 1351 - 135
7METMETLYSLYSchain GGG1 - 1371 - 137

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Components

#1: Protein
Recombination protein uvsY / Genetic recombination


Mass: 15865.247 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: uvsY / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04537

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1:1 UvsY (10 mg/mL, 150 mM sodium chloride, 20 mM HEPES, pH 7.5, 2 mM DTT) to 10% Jeffamine T-403, 10% Jeffamine ED-2003, 100 mM Tris-HCl, pH 8.0 in the presence of 750 uM dA3 oligonucleotide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 1, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→45.262 Å / Num. obs: 87352 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.55 % / Biso Wilson estimate: 67.95 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.104 / Rrim(I) all: 0.118 / Χ2: 1.045 / Net I/σ(I): 11.26 / Num. measured all: 397409
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.6-2.763.90.2841.7950.916351414113140762.03599.7
2.76-2.950.5751.0151.686047713294132931.15100
2.95-3.180.8360.4993.295618812317123150.565100
3.18-3.480.9610.2366.655186111348113470.268100
3.48-3.890.9890.11812.524717910308103080.133100
3.89-4.490.9960.06421.3741494906890680.072100
4.49-5.490.9980.0525.6135033766876680.056100
5.49-7.710.9980.04826.6227022595959580.055100
7.710.9990.02346.6514641334133190.02699.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4ZWR
Resolution: 2.6→45.262 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2363 3698 4.24 %
Rwork0.2023 83612 -
obs0.2037 87310 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.14 Å2 / Biso mean: 71.1781 Å2 / Biso min: 41.04 Å2
Refinement stepCycle: final / Resolution: 2.6→45.262 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5732 0 0 0 5732
Num. residues----732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075816
X-RAY DIFFRACTIONf_angle_d0.9737801
X-RAY DIFFRACTIONf_chiral_restr0.043868
X-RAY DIFFRACTIONf_plane_restr0.005979
X-RAY DIFFRACTIONf_dihedral_angle_d11.7222118
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3338X-RAY DIFFRACTION9.055TORSIONAL
12B3338X-RAY DIFFRACTION9.055TORSIONAL
13C3338X-RAY DIFFRACTION9.055TORSIONAL
14D3338X-RAY DIFFRACTION9.055TORSIONAL
15E3338X-RAY DIFFRACTION9.055TORSIONAL
16F3338X-RAY DIFFRACTION9.055TORSIONAL
17G3338X-RAY DIFFRACTION9.055TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5997-2.63390.38061430.36773219336298
2.6339-2.670.3541360.354831893325100
2.67-2.70810.35711430.349832283371100
2.7081-2.74850.39791450.333232453390100
2.7485-2.79150.33711400.320231713311100
2.7915-2.83720.30021400.310632223362100
2.8372-2.88620.31611400.294531963336100
2.8862-2.93860.31761410.282432513392100
2.9386-2.99510.29561370.266931983335100
2.9951-3.05630.30081400.27432373377100
3.0563-3.12270.30931420.264231753317100
3.1227-3.19530.29641450.267432623407100
3.1953-3.27520.2481430.233432013344100
3.2752-3.36370.31131420.235332143356100
3.3637-3.46270.25191440.229732023346100
3.4627-3.57440.26191440.204232203364100
3.5744-3.70210.25391440.214532413385100
3.7021-3.85030.27811420.206232123354100
3.8503-4.02540.22191440.175632153359100
4.0254-4.23750.18911420.153432193361100
4.2375-4.50270.18761420.156532013343100
4.5027-4.850.161400.143432243364100
4.85-5.33740.21621400.157832373377100
5.3374-6.10810.24691470.207532063353100
6.1081-7.68950.19411490.190732203369100
7.6895-45.26860.18591430.154132073350100
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)
12.152-0.5112-2.59441.36051.57455.7871-0.06020.4787-0.0196-0.06630.0636-0.2025-0.24550.50370.00050.37350.00490.01190.8368-0.06230.674631.258762.21121.8009
25.216-2.0498-2.99585.73091.8328.6628-0.1445-0.2110.04290.7308-0.0107-0.12870.63530.3520.02490.43190.0681-0.16440.5861-0.03010.615325.966368.689836.0637
34.26752.07820.88811.91562.83116.80230.1014-0.01160.54391.28880.2781-0.93380.7660.6214-0.22040.87970.0477-0.2211.0187-0.08820.896528.729174.60747.3521
43.80540.7824-2.6382.83291.04838.2862-0.07410.15880.10970.4244-0.12950.1685-0.4862-0.21310.3190.59160.1065-0.09270.5504-0.1260.664318.787973.064934.7644
51.2376-0.5366-2.2123.07141.98724.203-0.26340.716-0.0888-0.10910.03780.10960.3045-0.02170.52060.3379-0.0032-0.01671.0362-0.15880.655124.088257.6233-4.4244
62.0433-0.6966-0.50442.69131.89318.4804-0.14080.61470.2727-0.43880.07190.0249-0.68570.1372-0.07870.3862-0.00020.01380.76450.0160.623214.11768.4235-3.0287
72.2602-1.4163-3.1776.9970.74388.70130.2762-0.2765-0.38810.55510.2423-0.43260.1975-0.37190.0580.48110.0863-0.13340.5534-0.07630.717812.630275.664425.5123
82.4678-2.6262-4.2529.41543.88237.3789-0.5030.0675-0.64160.550.10671.3593-0.2865-2.03140.22430.71450.22910.0220.7775-0.08090.84267.524780.492136.5609
94.2508-1.86283.24221.8966-2.06193.2096-0.4435-0.44892.24730.6044-0.93610.8323-1.2331-1.26620.93240.83690.22320.0040.6980.01531.1088.166583.004432.3261
101.5498-1.9857-3.13675.9376.14619.2144-0.06990.39150.0863-0.110.1250.01530.1584-0.3671-0.04760.4038-0.0015-0.08110.9144-0.06470.662410.380461.0206-2.9897
112.24820.07940.02530.97980.78342.80320.52121.32730.3125-0.6886-0.48560.311-0.3899-1.83490.01210.55210.0634-0.13411.2637-0.0320.7364-9.194757.252-7.0273
122.9029-1.0113-3.78253.7470.89815.5085-0.39921.13910.1528-0.4233-0.35460.4220.5095-1.0610.2620.37860.0944-0.07061.07020.03830.55553.636256.4667-15.0413
133.76482.904-0.85443.40131.58135.05850.45230.15311.12110.0214-0.4280.3587-0.5489-0.82670.16110.37060.1114-0.02850.7518-0.05960.7989-2.849469.83787.4466
144.1247-0.9054-3.29955.95026.41458.9586-0.16450.2569-0.01520.6131-0.43640.69390.2575-0.76820.13550.38740.1197-0.02860.8448-0.00480.7191-6.317462.13427.7848
154.2945-3.878-4.31878.36074.32847.3314-0.20820.9211-0.5242-0.63280.137-0.03780.4921-0.82490.1980.55-0.098-0.06931.0559-0.28830.59736.499643.0196-13.9334
169.2979-0.656-3.1994.57091.7454.8474-0.13670.4475-0.8502-0.5510.4707-0.38650.681-0.95240.29340.6377-0.2645-0.06641.092-0.19550.7075-16.67338.28143.3459
174.5666-0.0515-1.92151.20290.1712.7708-0.1650.6661-0.1451-0.1018-0.12470.11670.2724-0.53970.1370.4695-0.0677-0.09711.0108-0.17370.604-8.621445.6671-1.9077
186.1342-3.5784-1.98517.3518-3.55144.85831.4548-0.10181.79490.15360.489-0.44110.33070.6199-0.07380.3466-0.23310.05390.9481-0.24650.7628-21.914360.689318.3335
197.3295-3.0966-5.49571.70431.99674.3224-0.09120.0809-0.3941-0.0690.1069-0.24740.3757-0.0053-0.17810.4527-0.062-0.08570.9708-0.17010.6765-7.442643.17396.2723
202.02280.5923-0.97322.0014-9.87819.0545-1.26550.7896-1.01950.1789-1.27060.2680.6367-0.6623-0.85921.10150.19830.01031.0103-0.48161.067112.459329.4083-11.8492
216.1113.3697-2.93963.1833-0.532.3034-0.48050.4647-0.81930.7965-0.35790.82040.1454-0.04320.20140.8497-0.1475-0.03640.81-0.03721.2001-9.678822.659218.028
221.49520.1499-1.122.6954-0.31320.9497-0.04650.148-0.7221-0.20210.1386-0.06480.4671-0.3189-0.08840.5788-0.1397-0.10970.8743-0.21220.7479-6.4730.33948.458
230.83930.5208-1.76843.18890.98035.59440.6768-0.26210.19511.2025-0.3262-1.165-0.97050.0343-0.00880.6350.01120.15190.7670.0880.8176-24.555837.488929.2578
244.48650.0097-0.99753.465-0.7366.3664-0.3514-0.392-0.79080.47910.5024-0.1630.4829-1.3926-0.06270.6946-0.1647-0.10261.12770.13490.83-11.063931.890322.4316
258.9983-0.1699-4.01691.8382-1.51225.5172-0.00590.8813-1.773-0.2666-0.1011-0.16570.78290.27460.16880.56750.03880.01860.744-0.29280.889811.14931.41063.3537
264.0185-0.58-0.65932.0385-1.27394.151-0.10390.0782-0.4799-0.23690.4413-0.55640.9690.12860.01030.75980.0695-0.06970.4917-0.04811.111413.358121.278523.9489
273.15020.9086-1.7711.8439-2.58263.79620.08310.0684-0.7759-0.44620.2289-0.0660.8140.3042-0.06070.7336-0.0096-0.10850.4804-0.14750.8916.417824.633716.3885
283.98150.43281.10243.9712-0.32214.24780.0217-0.871-0.42790.57480.339-0.8610.31130.1273-0.51750.5365-0.038-0.09430.80130.18910.6486-10.435825.376735.3423
299.75.1728-5.63726.6788-5.17164.46510.4216-1.0844-0.26060.3827-0.21440.55210.55250.1117-0.39750.8265-0.1167-0.06490.89030.1250.98072.223627.067533.6115
307.94355.0531-5.83.6554-4.57349.5961-0.17630.4481-1.1206-0.03980.1494-0.79650.43620.29090.06420.52020.08750.01820.616-0.25180.864318.765234.116510.9557
313.9341-0.8327-0.96680.3747-0.99936.71210.2726-0.0474-0.57570.06730.0058-0.38210.17240.7513-0.07340.66620.1903-0.13430.5966-0.04970.997723.147732.180629.0245
323.23031.5703-3.13154.32552.92628.87680.0344-1.2393-0.37351.1821-0.8175-1.60841.3304-0.6574-0.03420.84860.0568-0.15550.81430.1940.84158.21726.33744.8368
330.3451-0.27571.27463.01091.14577.565-0.4648-0.6485-0.67680.36140.2234-0.33670.9571-1.40880.11330.59660.0727-0.09290.96710.08270.5845.192726.316953.5907
343.65641.8411-2.19451.4581-3.28439.8750.2037-0.235-0.3080.40270.3744-0.1066-0.5626-0.2942-0.33020.63050.1983-0.04140.5771-0.06070.758418.49338.592729.7111
351.02880.88842.69069.54623.90177.3499-0.9447-0.3048-1.4002-1.04940.1062-0.3843-0.64570.4232-0.54490.44590.06260.12170.7439-0.13770.677228.320647.19736.1337
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:49)A1 - 49
2X-RAY DIFFRACTION2(chain A and resid 50:65)A50 - 65
3X-RAY DIFFRACTION3(chain A and resid 66:73)A66 - 73
4X-RAY DIFFRACTION4(chain A and resid 74:100)A74 - 100
5X-RAY DIFFRACTION5(chain A and resid 101:136)A101 - 136
6X-RAY DIFFRACTION6(chain B and resid 1:49)B1 - 49
7X-RAY DIFFRACTION7(chain B and resid 50:57)B50 - 57
8X-RAY DIFFRACTION8(chain B and resid 58:66)B58 - 66
9X-RAY DIFFRACTION9(chain B and resid 67:94)B67 - 94
10X-RAY DIFFRACTION10(chain B and resid 95:136)B95 - 136
11X-RAY DIFFRACTION11(chain C and resid 1:19)C1 - 19
12X-RAY DIFFRACTION12(chain C and resid 20:30)C20 - 30
13X-RAY DIFFRACTION13(chain C and resid 31:57)C31 - 57
14X-RAY DIFFRACTION14(chain C and resid 58:119)C58 - 119
15X-RAY DIFFRACTION15(chain C and resid 120:135)C120 - 135
16X-RAY DIFFRACTION16(chain D and resid 2:12)D2 - 12
17X-RAY DIFFRACTION17(chain D and resid 13:47)D13 - 47
18X-RAY DIFFRACTION18(chain D and resid 48:55)D48 - 55
19X-RAY DIFFRACTION19(chain D and resid 56:130)D56 - 130
20X-RAY DIFFRACTION20(chain D and resid 131:136)D131 - 136
21X-RAY DIFFRACTION21(chain E and resid 1:8)E1 - 8
22X-RAY DIFFRACTION22(chain E and resid 9:49)E9 - 49
23X-RAY DIFFRACTION23(chain E and resid 50:96)E50 - 96
24X-RAY DIFFRACTION24(chain E and resid 97:114)E97 - 114
25X-RAY DIFFRACTION25(chain E and resid 115:135)E115 - 135
26X-RAY DIFFRACTION26(chain F and resid 1:19)F1 - 19
27X-RAY DIFFRACTION27(chain F and resid 20:42)F20 - 42
28X-RAY DIFFRACTION28(chain F and resid 43:97)F43 - 97
29X-RAY DIFFRACTION29(chain F and resid 98:114)F98 - 114
30X-RAY DIFFRACTION30(chain F and resid 115:135)F115 - 135
31X-RAY DIFFRACTION31(chain G and resid 1:42)G1 - 42
32X-RAY DIFFRACTION32(chain G and resid 43:49)G43 - 49
33X-RAY DIFFRACTION33(chain G and resid 50:99)G50 - 99
34X-RAY DIFFRACTION34(chain G and resid 100:130)G100 - 130
35X-RAY DIFFRACTION35(chain G and resid 131:137)G131 - 137

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