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- PDB-5odn: Salinibacter ruber Single-Strand Binding protein -

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Basic information

Entry
Database: PDB / ID: 5odn
TitleSalinibacter ruber Single-Strand Binding protein
Components
  • DNA (5'-D(*TP*TP*T)-3')
  • DNA (5'-D(P*TP*TP*TP*T)-3')
  • Single-stranded DNA-binding protein
KeywordsDNA BINDING PROTEIN / Single-Strand Binding protein
Function / homology
Function and homology information


nucleoid / single-stranded DNA binding / DNA recombination / DNA replication / DNA repair
Similarity search - Function
Single-stranded DNA-binding protein / Single-strand binding protein family / Single-strand binding (SSB) domain profile. / Primosome PriB/single-strand DNA-binding / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA / Single-stranded DNA-binding protein
Similarity search - Component
Biological speciesSalinibacter ruber (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.598 Å
AuthorsPierechod, M. / Rothweiler, U.
Citation
Journal: To Be Published
Title: Salinibacter ruber Single-Strand Binding protein
Authors: Pierechod, M. / Rothweiler, U.
#1: Journal: Patent / Year: 2018
Title: Single-strand binding protein
Authors: Pierechod, M. / Willassen, N.P. / Rothweiler, U.
History
DepositionJul 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author
Revision 1.2Feb 3, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_patent / _citation.title
Revision 1.3Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Single-stranded DNA-binding protein
B: Single-stranded DNA-binding protein
C: Single-stranded DNA-binding protein
D: Single-stranded DNA-binding protein
E: Single-stranded DNA-binding protein
F: Single-stranded DNA-binding protein
G: Single-stranded DNA-binding protein
H: Single-stranded DNA-binding protein
I: DNA (5'-D(P*TP*TP*TP*T)-3')
M: DNA (5'-D(P*TP*TP*TP*T)-3')
J: DNA (5'-D(P*TP*TP*TP*T)-3')
K: DNA (5'-D(P*TP*TP*TP*T)-3')
N: DNA (5'-D(P*TP*TP*TP*T)-3')
P: DNA (5'-D(*TP*TP*T)-3')
Q: DNA (5'-D(P*TP*TP*TP*T)-3')
L: DNA (5'-D(*TP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)183,97816
Polymers183,97816
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.470, 123.500, 205.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Single-stranded DNA-binding protein / SSB


Mass: 21901.439 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salinibacter ruber (strain DSM 13855 / M31) (bacteria)
Gene: ssb, SRU_0523 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2S565
#2: DNA chain
DNA (5'-D(P*TP*TP*TP*T)-3')


Mass: 1171.814 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Salinibacter ruber (bacteria)
#3: DNA chain DNA (5'-D(*TP*TP*T)-3')


Mass: 867.621 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Salinibacter ruber (bacteria)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG 3350 27% w/v, Tris-HCl pH 8.0, MgCl2 0.25M, ammonium sulphate 1M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.598→50 Å / Num. obs: 79148 / % possible obs: 98.3 % / Redundancy: 2.3 % / CC1/2: 0.997 / Rrim(I) all: 0.08 / Net I/σ(I): 12.71
Reflection shellResolution: 2.598→2.76 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 12799 / CC1/2: 0.706 / Rrim(I) all: 0.594 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EYG
Resolution: 2.598→47.255 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.08 / Phase error: 25.37
RfactorNum. reflection% reflection
Rfree0.2426 3981 5.03 %
Rwork0.1897 --
obs0.1923 79127 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.598→47.255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6410 571 0 104 7085
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077133
X-RAY DIFFRACTIONf_angle_d0.8479755
X-RAY DIFFRACTIONf_dihedral_angle_d16.7784069
X-RAY DIFFRACTIONf_chiral_restr0.0481078
X-RAY DIFFRACTIONf_plane_restr0.0041176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5984-2.630.30391480.28032685X-RAY DIFFRACTION97
2.63-2.66330.33911320.28592646X-RAY DIFFRACTION99
2.6633-2.69840.33981740.29172685X-RAY DIFFRACTION99
2.6984-2.73530.40121400.29562713X-RAY DIFFRACTION99
2.7353-2.77440.3061260.28912632X-RAY DIFFRACTION98
2.7744-2.81580.31631460.27292741X-RAY DIFFRACTION97
2.8158-2.85980.28771400.26942578X-RAY DIFFRACTION97
2.8598-2.90670.31731550.25452752X-RAY DIFFRACTION98
2.9067-2.95680.29831380.23542645X-RAY DIFFRACTION99
2.9568-3.01060.28221520.23742727X-RAY DIFFRACTION99
3.0106-3.06850.29631430.22822664X-RAY DIFFRACTION99
3.0685-3.13110.2851710.22562683X-RAY DIFFRACTION98
3.1311-3.19910.29841240.21562681X-RAY DIFFRACTION98
3.1991-3.27350.27031530.22252701X-RAY DIFFRACTION99
3.2735-3.35540.28931460.20912685X-RAY DIFFRACTION98
3.3554-3.44610.29351430.18792694X-RAY DIFFRACTION98
3.4461-3.54740.28511670.16852656X-RAY DIFFRACTION98
3.5474-3.66190.20361020.16632705X-RAY DIFFRACTION99
3.6619-3.79270.19421420.15812718X-RAY DIFFRACTION99
3.7927-3.94450.21481590.15622686X-RAY DIFFRACTION99
3.9445-4.12390.18521240.15932724X-RAY DIFFRACTION99
4.1239-4.34120.24931220.14962660X-RAY DIFFRACTION97
4.3412-4.6130.17931290.13692683X-RAY DIFFRACTION97
4.613-4.96880.17811410.13892634X-RAY DIFFRACTION97
4.9688-5.46820.1861340.14822750X-RAY DIFFRACTION99
5.4682-6.25790.21031380.17292717X-RAY DIFFRACTION99
6.2579-7.87840.25731290.20962643X-RAY DIFFRACTION97
7.8784-47.26330.22021630.21872658X-RAY DIFFRACTION98
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)
16.1193-2.547-2.88627.63444.63943.69280.3134-0.5586-0.253-0.2519-0.04060.2631-0.08850.2017-0.22810.2887-0.0804-0.05960.38920.12510.1814-32.3227-14.000629.0639
22.12294.13347.02225.710.40269.6574-0.44660.8342-0.3547-0.26370.73070.352-0.1445-0.2532-0.38580.3386-0.04670.04460.52810.06530.3029-38.5917-21.408311.1889
38.1328-0.98362.73938.14-4.41828.0261-0.0852-0.2529-0.26980.21060.143-0.68130.00510.1459-0.09580.2158-0.0216-0.01180.2794-0.09210.268-29.0216-20.882123.2329
48.82984.9266-2.10758.079-0.66143.76350.3144-0.0168-0.46830.2966-0.13380.13150.3154-0.2061-0.22560.2797-0.0121-0.11510.44260.05720.1663-37.0243-23.60826.8869
57.95695.9141-5.43087.5066-4.57466.61560.00480.08460.21660.010.37180.28390.09820.3105-0.37630.3111-0.017-0.08310.38210.00590.2243-34.5514-18.761826.4782
67.1223-3.4352-1.37375.31953.72134.7063-0.0639-0.14020.2062-0.48190.47810.16020.08320.1762-0.40240.3076-0.0848-0.10870.29890.04720.3007-72.336-35.435210.3659
74.5709-6.10173.16188.3197-6.25298.83490.2359-0.3076-0.44380.0686-0.09870.00390.1096-0.0207-0.17480.3203-0.1434-0.03320.3525-0.01470.4064-72.1705-44.86659.7574
86.1901-2.92470.87029.7024-3.47823.47050.13830.4679-0.2714-0.1636-0.2918-0.22360.14640.34360.17750.2864-0.0975-0.10520.3049-0.09120.3633-70.6915-43.71475.1291
98.3845-1.19-2.07784.96920.50388.10450.32920.2576-0.2333-0.3323-0.30760.89860.2317-1.0069-0.03590.338-0.0516-0.11280.3821-0.05860.379-76.707-38.02939.665
107.22673.2408-0.10237.7648-1.27566.26530.09091.19650.0352-0.44330.43440.68990.5116-1.1678-0.42010.3918-0.0724-0.18090.478-0.05250.2899-77.9196-39.92148.0979
111.65820.2418-1.11953.426-0.47813.61670.2117-0.53590.13390.2643-0.01310.09650.2596-0.1545-0.23810.3471-0.1362-0.10330.4499-0.07140.336-74.2632-35.960828.1951
126.9705-0.46682.11229.3825-4.37277.77340.1628-0.23240.31890.4475-0.17140.5832-0.2621-0.26120.07940.2414-0.08960.06040.3781-0.09070.3721-79.6828-31.001127.1401
136.26861.9112-0.16468.3091-0.97062.77770.0714-0.1533-0.19410.42650.08980.06860.3292-0.3996-0.1490.261-0.0518-0.00170.4293-0.00970.1062-80.6572-39.986524.1178
145.29135.00461.47946.58023.79834.31720.3743-0.5990.07220.3324-0.28070.07740.0626-0.0792-0.08970.4662-0.1368-0.06730.543-0.0440.3599-76.3249-36.594624.7092
151.90851.6312-0.74252.32462.10518.8556-0.1546-0.7859-0.39590.4111-0.11730.20980.85390.26760.29020.3993-0.0233-0.08440.65430.04160.4484-62.4514-28.268427.7883
167.0432-1.04654.52444.4081-1.14197.5021-0.16991.2449-0.8142-0.13370.1964-0.3191-0.2481.1683-0.07410.3564-0.08650.09230.4746-0.06790.5407-44.6177-30.790512.8354
178.7366-0.72512.48235.7998-0.34799.60360.18620.4485-1.0377-0.49840.1685-0.50790.75710.2434-0.29280.3092-0.09310.060.3352-0.10640.4896-47.396-33.60312.5288
186.97815.60981.47827.89161.65883.97880.7347-0.43330.16790.8997-0.5371-0.4076-0.11310.1693-0.23170.3361-0.0034-0.01750.3656-0.05960.3806-47.4908-19.101116.7701
196.27947.45392.1348.80631.63232.99480.1603-0.162-0.50780.33320.0537-0.54130.17640.1793-0.2730.21970.0128-0.04660.3173-0.04220.4283-51.1457-26.626616.1527
202.896-1.65011.67283.18571.58543.6118-0.4206-0.12650.03820.31530.1727-0.4804-0.05760.58960.15470.3112-0.0525-0.09590.58420.10630.3221-13.5472-3.701940.7584
216.511-2.54475.9987.135-4.26657.27220.24780.33180.0839-0.3774-0.23450.4826-0.25760.6873-0.09430.3297-0.11660.01230.56820.03890.4782-18.38110.929323.8574
225.3263-1.1773-0.00987.3366-3.08687.6728-0.0259-0.2722-0.2657-0.1120.2286-0.54410.45810.0401-0.2610.2581-0.1326-0.11760.5146-0.06140.5007-10.8617-4.75633.2349
232.9872-0.3670.44642.89362.60866.89310.0754-0.61580.08590.59390.0951-0.9432-0.31040.4855-0.20050.3797-0.1652-0.08810.61250.0280.406-15.2912-0.316139.3928
246.3361-0.024-1.92566.51623.82847.1605-0.27780.09750.2657-0.72220.07270.3476-0.51240.12290.23990.2994-0.0484-0.09810.26650.11320.2582-63.9225-19.736113.2899
252.7228-2.38910.87376.3405-5.4183.42390.0675-0.2378-0.17440.7430.19150.4555-1.18560.0918-0.19760.4397-0.1041-0.02460.3509-0.0230.5228-62.2889-11.630517.1088
266.6103-0.31390.923.86230.67642.91420.1678-0.49310.67020.02370.2009-0.1097-0.5971-0.2325-0.44510.4681-0.0617-0.0350.3774-0.02290.5603-65.1662-11.581616.2554
277.1695-1.6212-2.14013.85290.04027.76990.31870.4971.1454-0.3803-0.3133-0.3892-1.12530.6345-0.08220.5064-0.111-0.06460.33430.10080.5309-58.4955-11.428711.9896
287.48391.5561-4.17358.5448-2.71795.5951-0.02910.97660.7783-0.36790.03780.4942-0.2277-0.3733-0.03310.3505-0.0248-0.12750.51470.06710.3775-63.47-15.064912.6262
295.5481-0.1126-1.753.5956-0.18791.73450.0183-0.7691-0.64530.5541-0.06940.0540.2648-0.20840.08790.4566-0.1168-0.06760.63520.04860.257-35.908-18.316246.0122
307.0589-1.78564.39436.2596-1.04317.7903-0.1399-0.32480.11320.327-0.08570.0902-0.2805-0.43560.20690.3409-0.15210.08860.5694-0.01430.2593-43.9453-12.702940.2018
315.3905-0.3301-0.94985.8570.98165.07850.1062-0.7944-0.30610.89870.1564-0.26230.5637-0.0353-0.27030.3936-0.0917-0.03460.59450.11720.2312-37.8707-17.639943.2455
326.104-2.438-2.94916.49491.7442.50830.19670.2670.1279-0.0073-0.33370.1086-0.3842-0.23580.03570.323-0.0992-0.07520.44770.03950.2114-29.37621.972534.5431
333.5233-0.2177-0.84369.9654-5.19527.0846-0.0394-0.23170.36060.82290.13050.8297-0.2575-0.3265-0.0760.3334-0.09310.05120.4599-0.12850.4068-34.488611.891437.6626
346.69786.776-3.27899.2409-1.66972.5978-0.26530.33040.0148-0.01660.2531-0.2194-0.1783-0.01790.00460.281-0.0444-0.05620.51950.10180.333-24.507710.39634.5884
358.837-7.4087-1.5612.13078.33586.38080.0781-2.21731.09210.17230.00070.4468-1.54920.951-0.30360.8622-0.16690.14081.0928-0.39580.8909-62.8736-9.189429.6402
362.13014.91051.8767.56366.98677.4014-0.288-0.514-0.183-0.3593-0.09040.5024-0.9986-0.1370.43280.4640.06450.14960.6993-0.06420.5218-52.8213-8.818340.0579
372.08348.5119.71696.28016.92328.0124-1.65812.62080.0641-2.45670.69850.53680.7569-0.15470.70371.0335-0.42910.07261.5264-0.38650.8612-48.6322-31.2028-2.2379
382.0155-2.1607-9.12796.79723.64788.80450.1606-1.5127-0.9909-0.290.0248-0.39140.59131.7477-0.26940.68360.1392-0.20520.72930.02120.9669-64.5164-53.215310.1679
399.1989-9.3333-0.40172.02426.97772.12920.66890.61711.0715-0.3455-1.11712.5974-0.8464-2.25950.53960.86150.01350.0020.8060.05471.3068-89.8854-24.167323.4255
401.99397.130.93599.1321-6.80572.00051.2677-3.4707-2.0786-0.4111-2.2699-2.9870.23581.31030.96110.78370.1641-0.17881.3486-0.00941.4909-20.6635-30.04427.5824
416.9214-7.69980.00312.06944.07947.16950.75431.25950.0108-2.2333-0.71570.1828-0.86-0.5042-0.00620.8796-0.09460.05891.017-0.04130.5983-9.728-1.77821.2261
422.01479.55771.9482.02432.00189.49671.8808-4.58350.70642.6696-3.19140.4751-1.17721.68211.13021.1782-0.16690.18861.2204-0.02441.0579-32.139711.598652.0475
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 18 )
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 27 )
3X-RAY DIFFRACTION3chain 'A' and (resid 28 through 69 )
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 93 )
5X-RAY DIFFRACTION5chain 'A' and (resid 94 through 108 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 18 )
7X-RAY DIFFRACTION7chain 'B' and (resid 19 through 46 )
8X-RAY DIFFRACTION8chain 'B' and (resid 47 through 74 )
9X-RAY DIFFRACTION9chain 'B' and (resid 75 through 87 )
10X-RAY DIFFRACTION10chain 'B' and (resid 88 through 109 )
11X-RAY DIFFRACTION11chain 'C' and (resid -1 through 27 )
12X-RAY DIFFRACTION12chain 'C' and (resid 28 through 69 )
13X-RAY DIFFRACTION13chain 'C' and (resid 70 through 93 )
14X-RAY DIFFRACTION14chain 'C' and (resid 94 through 108 )
15X-RAY DIFFRACTION15chain 'D' and (resid -6 through 13 )
16X-RAY DIFFRACTION16chain 'D' and (resid 14 through 49 )
17X-RAY DIFFRACTION17chain 'D' and (resid 50 through 74 )
18X-RAY DIFFRACTION18chain 'D' and (resid 75 through 93 )
19X-RAY DIFFRACTION19chain 'D' and (resid 94 through 108 )
20X-RAY DIFFRACTION20chain 'E' and (resid 1 through 27 )
21X-RAY DIFFRACTION21chain 'E' and (resid 28 through 46 )
22X-RAY DIFFRACTION22chain 'E' and (resid 47 through 74 )
23X-RAY DIFFRACTION23chain 'E' and (resid 75 through 109 )
24X-RAY DIFFRACTION24chain 'F' and (resid 1 through 18 )
25X-RAY DIFFRACTION25chain 'F' and (resid 19 through 47 )
26X-RAY DIFFRACTION26chain 'F' and (resid 48 through 69 )
27X-RAY DIFFRACTION27chain 'F' and (resid 70 through 93 )
28X-RAY DIFFRACTION28chain 'F' and (resid 94 through 109 )
29X-RAY DIFFRACTION29chain 'G' and (resid 1 through 27 )
30X-RAY DIFFRACTION30chain 'G' and (resid 28 through 69 )
31X-RAY DIFFRACTION31chain 'G' and (resid 70 through 108 )
32X-RAY DIFFRACTION32chain 'H' and (resid 0 through 18 )
33X-RAY DIFFRACTION33chain 'H' and (resid 19 through 74 )
34X-RAY DIFFRACTION34chain 'H' and (resid 75 through 108 )
35X-RAY DIFFRACTION35chain 'I' and (resid 1 through 4 )
36X-RAY DIFFRACTION36chain 'M' and (resid 1 through 4 )
37X-RAY DIFFRACTION37chain 'J' and (resid 1 through 4 )
38X-RAY DIFFRACTION38chain 'K' and (resid 1 through 4 )
39X-RAY DIFFRACTION39chain 'N' and (resid 1 through 4 )
40X-RAY DIFFRACTION40chain 'P' and (resid 1 through 3 )
41X-RAY DIFFRACTION41chain 'Q' and (resid 1 through 4 )
42X-RAY DIFFRACTION42chain 'L' and (resid 1 through 3 )

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