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

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Basic information

Entry
Database: PDB / ID: 4zwr
TitleCrystal Structure of the Bacteriophage T4 recombination mediator protein UvsY, Lattice Type II
ComponentsRecombination protein uvsY
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 / SAD / Resolution: 3.3857 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 1.5Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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)128,5547
Polymers128,5547
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17060 Å2
ΔGint-152 kcal/mol
Surface area44060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.600, 123.830, 302.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain C and (resseq 0:136 )
21chain B and (resseq 0:135 )
31chain A and (resseq 1:65 or resseq 73:135 )
41chain D and (resseq 0:134 )
51chain E and (resseq 0:136 )
61chain F and (resseq 0:136 )
12chain C
22chain B
32chain A and (resseq 1:65 or resseq 73:135 )
42chain D
52chain E
62chain F

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111HISHISGLYGLYchain C and (resseq 0:136 )CC0 - 13620 - 156
211HISHISALAALAchain B and (resseq 0:135 )BB0 - 13520 - 155
311MSEMSESERSERchain A and (resseq 1:65 or resseq 73:135 )AA1 - 6521 - 85
321PHEPHEALAALAchain A and (resseq 1:65 or resseq 73:135 )AA73 - 13593 - 155
411HISHISGLUGLUchain D and (resseq 0:134 )DD0 - 13420 - 154
511HISHISGLYGLYchain E and (resseq 0:136 )EE0 - 13620 - 156
611HISHISGLYGLYchain F and (resseq 0:136 )FF0 - 13620 - 156
112HISHISGLYGLYchain CCC0 - 13620 - 156
212HISHISALAALAchain BBB0 - 13520 - 155
312MSEMSESERSERchain A and (resseq 1:65 or resseq 73:135 )AA1 - 6521 - 85
322PHEPHEALAALAchain A and (resseq 1:65 or resseq 73:135 )AA73 - 13593 - 155
412HISHISGLUGLUchain DDD0 - 13420 - 154
512HISHISGLYGLYchain EEE0 - 13620 - 156
612HISHISGLYGLYchain FFF0 - 13620 - 156

NCS ensembles :
ID
1
2

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Components

#1: Protein
Recombination protein uvsY


Mass: 18364.889 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: uvsY / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04537
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 1:1 Se-Met-labeled UvsY (12 mg/mL in 0.5 M sodium chloride, 15 mM HEPES, pH 8.2, 2 mM DTT) to 18% MPD, 225 mM sodium chloride, 0.1 M MES, pH 6.4, sample subjected to reductive alkylation ...Details: 1:1 Se-Met-labeled UvsY (12 mg/mL in 0.5 M sodium chloride, 15 mM HEPES, pH 8.2, 2 mM DTT) to 18% MPD, 225 mM sodium chloride, 0.1 M MES, pH 6.4, sample subjected to reductive alkylation with formaldehyde prior to crystallization

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 8, 2010
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.3857→20 Å / Num. obs: 14057 / % possible obs: 63.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 87.48 Å2 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.063 / Rrim(I) all: 0.163 / Χ2: 1.396 / Net I/av σ(I): 16.8 / Net I/σ(I): 6.9 / Num. measured all: 93454
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
3.3857-3.526.60.9381.761590.7850.3930.6137.4
3.52-3.666.80.7073590.8850.2910.65716.70.766
3.66-3.836.80.7056820.8670.290.72731.20.763
3.83-4.036.90.64810410.9090.2670.77747.90.702
4.03-4.2870.38713390.9690.1570.97361.60.418
4.28-4.66.90.29516790.990.1231.0476.60.32
4.6-5.066.40.21120290.9910.0891.27192.50.23
5.06-5.786.40.22722150.9890.0951.26699.70.246
5.78-7.226.60.17622410.9840.0731.6331000.191
7.22-206.60.1123130.9930.0462.5999.60.12

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
PHASERphasing
RESOLVEphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 3.3857→19.911 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.77 / Stereochemistry target values: ML
Details: THE X-RAY DIFFRACTION DATA EXHIBITED STRONG ANISOTROPY. REFINEMENT WAS PERFORMED AGAINST ELLIPTICALLY TRUNCATED DATA (RESOLUTION LIMITS OF 1/5.0, 1/3.8, AND 1/3.4 A IN A*, B*, C*, ...Details: THE X-RAY DIFFRACTION DATA EXHIBITED STRONG ANISOTROPY. REFINEMENT WAS PERFORMED AGAINST ELLIPTICALLY TRUNCATED DATA (RESOLUTION LIMITS OF 1/5.0, 1/3.8, AND 1/3.4 A IN A*, B*, C*, RESPECTIVELY) CORRECTED BY ANISOTROPIC SCALE FACTORS AND AN ISOTROPIC B OF -52.54 A2 USING THE UCLA DIFFRACTION ANISOTROPY SERVER (STRONG ET AL., 2006).
RfactorNum. reflection% reflection
Rfree0.2665 698 5 %
Rwork0.2391 13260 -
obs0.2405 13958 61.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 291.64 Å2 / Biso mean: 95.6672 Å2 / Biso min: 32.56 Å2
Refinement stepCycle: final / Resolution: 3.3857→19.911 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6850 0 0 0 6850
Num. residues----926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0016946
X-RAY DIFFRACTIONf_angle_d0.3339379
X-RAY DIFFRACTIONf_chiral_restr0.0131079
X-RAY DIFFRACTIONf_plane_restr0.0011195
X-RAY DIFFRACTIONf_dihedral_angle_d9.0042405
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11C1029X-RAY DIFFRACTIONPOSITIONAL0.012
12B1029X-RAY DIFFRACTIONPOSITIONAL0.012
13A968X-RAY DIFFRACTIONPOSITIONAL0.016
14D1026X-RAY DIFFRACTIONPOSITIONAL0.011
15E1018X-RAY DIFFRACTIONPOSITIONAL0.012
16F965X-RAY DIFFRACTIONPOSITIONAL0.013
21C1029X-RAY DIFFRACTIONPOSITIONAL0.012
22B1029X-RAY DIFFRACTIONPOSITIONAL0.012
23A968X-RAY DIFFRACTIONPOSITIONAL0.016
24D1026X-RAY DIFFRACTIONPOSITIONAL0.011
25E1018X-RAY DIFFRACTIONPOSITIONAL0.012
26F965X-RAY DIFFRACTIONPOSITIONAL0.013
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3857-3.64560.3719350.36293714069
3.6456-4.00980.4088700.32541513158335
4.0098-4.58390.28581400.24262835297566
4.5839-5.7520.2812100.24974110432095
5.752-19.91160.2282430.21364431467499
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)
10.1179-0.14720.03510.6881-0.30560.13950.1054-0.5676-0.45750.12890.30030.171-0.2182-0.5859-0.00030.9158-0.15770.05290.81550.10580.6377-1.132465.5804133.7272
20.47320.6088-0.54980.852-0.81620.94050.24820.4787-0.7565-0.39150.85011.01981.3069-1.33680.19410.9733-0.361-0.11750.69380.28280.7764-14.144865.2123100.7164
30.61520.0017-0.56180.2161-0.18910.6846-0.14220.00070.34530.3016-0.2018-0.0478-0.28030.5026-0.00231.0326-0.0128-0.04370.73410.03610.61086.708370.9212136.3034
40.66850.3555-0.52880.3058-0.18610.43890.0322-0.66950.55590.6129-0.14910.4416-0.3636-0.83050.00550.89430.09050.10980.5884-0.15940.52191.438183.1172127.3602
51.5005-1.443-0.03813.95950.67965.1484-0.15420.04080.0962-0.31020.00740.6913-0.6005-0.6099-0.81390.52470.23620.0258-0.01510.29390.759-11.723481.762795.7056
60.390.1579-0.64560.1716-0.33131.06620.2758-0.31720.13890.3103-0.4797-0.3736-0.06840.6926-0.11140.96250.0039-0.15170.4811-0.08970.490411.183482.9596129.2403
70.2148-0.11320.03650.5642-0.48340.43820.0349-0.18690.21620.1749-0.0263-0.1113-0.0950.22371.33080.9286-0.5608-0.38040.7994-0.56650.990424.656395.7631120.925
80.57670.1886-0.62811.3725-0.3042.92220.1166-0.1240.5198-0.0413-0.1606-0.1922-0.67150.496-0.29960.67070.02920.0822-0.0041-0.11290.60177.194190.6729105.9108
90.5151-0.04520.56760.8844-0.42252.95390.116-0.14950.19040.29540.1109-0.1861-0.01430.6446-0.6660.7707-0.3455-0.48580.4032-0.23810.741322.105786.2017120.4112
100.7335-0.0646-0.25570.00130.01830.0865-0.0460.0188-0.10410.02270.0249-0.2041-0.01160.22870.8090.2043-0.282-0.27191.248-0.09761.27139.482884.8334110.1101
110.7293-0.0298-0.98211.22220.50582.55140.0241-0.45650.14710.26720.2352-0.4606-0.40110.85450.04420.7807-0.54450.0140.35970.05180.635425.449588.5911105.5173
120.5206-0.12220.02590.87650.51940.32430.08990.47740.4186-0.6994-0.4523-0.7609-0.3780.1853-0.15840.7984-0.39780.09460.5880.2550.370812.392990.310672.5386
131.28060.3455-0.03250.66790.53812.8731-0.0266-0.30.0290.52410.0719-0.41770.13210.9760.18740.0401-0.51110.00080.67810.11490.580328.435880.1025104.8499
140.10640.0019-0.07550.06130.00680.05440.01460.044-0.03630.02990.0043-0.09910.03040.09440.08770.11270.0927-0.19741.61540.04190.897943.068464.4921104.2104
150.67410.08580.10690.39940.05940.91260.11710.1666-0.02290.02880.0004-0.5099-0.14640.67430.16490.0553-0.03530.16071.16890.01930.73131.558475.228189.5858
160.34340.64210.21841.23270.28690.2164-0.3347-0.4367-0.31160.6453-0.2854-0.36940.88410.3665-0.02290.92240.29330.05761.12070.02650.682331.071466.606899.1114
170.05770.01270.00430.18460.01050.08120.3859-0.12460.3251-0.06790.2726-0.7013-0.11670.4391-0.00091.08970.46480.07350.80890.10350.939532.406245.8123104.027
181.2853-0.1501-0.1080.940.80741.58180.30210.19-0.4011-0.0808-0.0144-0.22760.52650.16930.20540.79680.6023-0.08260.8879-0.20440.644529.458357.155187.6673
191.49770.86040.6151.05861.28111.81230.0788-0.51670.22670.0036-0.51540.31670.45810.0154-0.51990.59180.51680.01610.6483-0.19070.850924.373153.709798.0953
202.71181.56861.68522.36490.13974.5456-0.25390.5084-0.1609-0.84930.3860.06420.6336-0.20470.4131.323-0.5170.19170.66580.18660.733513.036139.1096110.6504
210.32650.05-0.31770.3905-0.07710.3415-0.1734-0.3903-0.58330.43050.0820.09210.3532-0.50130.00061.11210.03180.03630.7904-0.18480.87218.220745.418993.9794
220.5672-0.56850.19060.5731-0.27070.30490.324-0.89710.0873-0.0312-0.05120.43250.2071-0.41160.05051.0465-0.53910.43151.0464-0.41121.151412.588148.4592106.9696
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 65 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 90 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 91 through 135 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 65 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 66 through 90 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 91 through 135 )B0
7X-RAY DIFFRACTION7chain 'C' and (resid 0 through 17 )C0
8X-RAY DIFFRACTION8chain 'C' and (resid 18 through 90 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 91 through 136 )C0
10X-RAY DIFFRACTION10chain 'D' and (resid 0 through 17 )D0
11X-RAY DIFFRACTION11chain 'D' and (resid 18 through 65 )D0
12X-RAY DIFFRACTION12chain 'D' and (resid 66 through 79 )D0
13X-RAY DIFFRACTION13chain 'D' and (resid 80 through 134 )D0
14X-RAY DIFFRACTION14chain 'E' and (resid 0 through 17 )E0
15X-RAY DIFFRACTION15chain 'E' and (resid 18 through 79 )E0
16X-RAY DIFFRACTION16chain 'E' and (resid 80 through 136 )E0
17X-RAY DIFFRACTION17chain 'F' and (resid 0 through 17 )F0
18X-RAY DIFFRACTION18chain 'F' and (resid 18 through 79 )F0
19X-RAY DIFFRACTION19chain 'F' and (resid 80 through 136 )F0
20X-RAY DIFFRACTION20chain 'G' and (resid 1 through 20 )G0
21X-RAY DIFFRACTION21chain 'G' and (resid 21 through 91 )G0
22X-RAY DIFFRACTION22chain 'G' and (resid 92 through 133 )G0

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