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- PDB-7vum: Crystal structure of SSB complexed with que -

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Basic information

Entry
Database: PDB / ID: 7vum
TitleCrystal structure of SSB complexed with que
ComponentsSingle-stranded DNA-binding protein
KeywordsDNA BINDING PROTEIN / single-strand DNA binding protein
Function / homology
Function and homology information


nucleoid / enzyme activator activity / 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, OB-fold
Similarity search - Domain/homology
3,5,7,3',4'-PENTAHYDROXYFLAVONE / Single-stranded DNA-binding protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.319 Å
AuthorsLin, E.S. / Huang, Y.H. / Huang, C.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int J Mol Sci / Year: 2022
Title: A Complexed Crystal Structure of a Single-Stranded DNA-Binding Protein with Quercetin and the Structural Basis of Flavonol Inhibition Specificity.
Authors: Lin, E.S. / Luo, R.H. / Huang, C.Y.
History
DepositionNov 3, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4005
Polymers55,0974
Non-polymers3021
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-16 kcal/mol
Surface area20590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.277, 60.277, 131.385
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 13774.341 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: ssb, PA4232 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P40947
#2: Chemical ChemComp-QUE / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / QUERCETIN


Mass: 302.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.5 Å3/Da / Density % sol: 50.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 4000, 100mM MES Sodium Salt pH 6.5, 200mM Magnesium Chloride

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.975 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.319→30 Å / Num. obs: 23123 / % possible obs: 99.9 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 18.1
Reflection shellResolution: 2.319→2.4 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2309 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YUO

5yuo


Resolution: 2.319→27.801 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 27.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2497 1156 5.01 %
Rwork0.1957 21934 -
obs0.1985 23090 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.34 Å2 / Biso mean: 65.116 Å2 / Biso min: 23.66 Å2
Refinement stepCycle: final / Resolution: 2.319→27.801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3089 0 22 64 3175
Biso mean--133.54 56.83 -
Num. residues----392
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.3191-2.42460.34371400.25312735
2.4246-2.55240.29661680.23792709
2.5524-2.71220.30631320.22562773
2.7122-2.92140.28071470.22022716
2.9214-3.2150.30941060.20872800
3.215-3.67930.24261500.18892745
3.6793-4.6320.20741710.17312721
4.632-27.8010.23491420.18522735
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)
12.2825-0.50733.54935.1112.0317.01940.26630.1226-0.1573-0.086-0.1448-0.066-0.1611-0.7766-0.06270.26030.01930.06280.29850.02560.24644.982-10.9-2.398
24.76391.4082.85994.6271-2.39384.5535-0.6176-0.08351.2709-1.16850.50090.7758-1.07390.55110.30060.96020.0946-0.13550.80080.00670.4436-2.8260.891-16.809
36.2088-0.33951.08296.1733-0.09522.9949-0.1068-0.2756-0.1560.2438-0.02720.239-0.1532-0.97480.10380.31870.08690.0150.4230.03750.303-2.519-11.57-4.054
43.37471.4983-0.21035.36060.70742.5434-0.2007-0.3910.4615-0.1020.4810.4232-0.7931-0.216-0.27960.46540.1926-0.07770.3684-0.01770.39551.4720.1530.665
53.85911.77360.54122.82152.89536.42540.15220.05080.1491-0.2130.1452-0.3203-0.5399-0.2099-0.16010.34690.10270.00690.35430.07680.25364.021-6.251-4.122
67.22661.52650.46045.3514-0.53015.8295-0.038-0.47090.54670.44460.12260.1474-0.671-0.2226-0.09590.33110.0860.00860.2609-0.0130.348214.647-7.0958.196
79.98151.1444.01344.1709-3.01897.98120.02430.9121-1.33661.69741.23210.64310.3773-0.1602-0.93511.02590.2897-0.0740.47550.02220.5610.688-6.59627.325
85.60872.9335-2.85015.7155-3.34362.25370.09820.35460.5677-0.01970.4820.2611-0.1759-0.1526-0.59540.530.099-0.02710.3328-0.04180.42214.298-0.837.529
91.97190.67810.33470.27060.05253.1098-0.1696-1.1568-0.10080.3285-0.1237-0.6095-0.46890.1283-0.33060.80090.384-0.57910.52720.14010.186219.67-10.40821.293
108.7172.75321.36084.9274-0.01353.80140.4156-0.63360.40390.2846-0.0831-0.5283-0.274-0.0146-0.37730.42060.06870.03280.3959-0.09890.369512.373-5.32811.809
114.4135-0.459-2.75444.36565.71368.54150.09530.0053-1.15080.62340.21810.44111.10270.77470.23571.45550.93610.37091.0487-0.55591.3675-5.3514.02916.806
128.22482.24391.53795.641-1.12285.36220.6553-0.5139-0.55810.5632-0.37460.202-0.0419-0.1803-0.17260.54020.1406-0.06560.40220.01220.339210.676-8.78612.091
136.49461.6597-0.48042.6918-0.49324.3238-0.36350.07920.7039-0.63480.2266-0.4214-0.12540.64480.12840.5220.06570.12530.41370.08460.540829.57-17.104-10.054
148.2102-0.35261.39794.1136-1.87536.94340.04050.44970.8166-0.6399-0.4042-1.32420.27650.80910.31970.36750.0760.10980.43770.05850.566631.321-17.236-3.575
153.56251.42621.26866.71493.20375.1446-0.6040.38260.4316-0.97250.4012-0.27540.05670.2030.01460.51790.09540.14270.58010.00220.269325.051-21.991-8.263
166.8278-1.57650.90328.10622.22084.14260.57070.7326-0.1429-0.9161-0.73640.30160.47090.2945-0.07950.5640.0840.0450.54530.08640.30725.921-21.032-9.29
172.9225-0.92691.14436.067-0.11353.1696-0.2697-0.4808-1.21940.14640.42880.61110.3365-0.2773-0.15140.37820.15960.12210.46860.14210.705313.507-33.9542.764
188.2161.8225-1.87495.5508-0.10057.9632-0.84060.6194-1.2112-1.2937-0.64540.21740.58870.2071.26610.65880.02450.11880.398-0.05340.555312.551-31.456-8.354
196.64741.83061.17317.4352-3.31049.17420.3181-0.709-1.9963-0.05180.33260.96930.9655-0.8288-0.47530.52550.05910.00540.47210.24141.019.909-34.4090.285
201.1862-0.41740.5111.9969-0.1661.9771-0.3493-0.1392-1.54440.03420.17011.02210.71630.03240.06010.47430.00340.05030.29340.01530.796418.923-35.328-2.817
219.1021-5.6171-0.01666.62210.06962.32140.4498-1.221-1.1797-0.3555-0.00330.42470.35030.0922-0.30230.47370.0427-0.05210.38450.11080.417715.963-30.9860.964
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:18 )A3 - 18
2X-RAY DIFFRACTION2( CHAIN A AND RESID 19:27 )A19 - 27
3X-RAY DIFFRACTION3( CHAIN A AND RESID 28:75 )A28 - 75
4X-RAY DIFFRACTION4( CHAIN A AND RESID 76:94 )A76 - 94
5X-RAY DIFFRACTION5( CHAIN A AND RESID 95:113 )A95 - 113
6X-RAY DIFFRACTION6( CHAIN B AND RESID 4:18 )B4 - 18
7X-RAY DIFFRACTION7( CHAIN B AND RESID 19:27 )B19 - 27
8X-RAY DIFFRACTION8( CHAIN B AND RESID 28:60 )B28 - 60
9X-RAY DIFFRACTION9( CHAIN B AND RESID 61:70 )B61 - 70
10X-RAY DIFFRACTION10( CHAIN B AND RESID 71:88 )B71 - 88
11X-RAY DIFFRACTION11( CHAIN B AND RESID 89:95 )B89 - 95
12X-RAY DIFFRACTION12( CHAIN B AND RESID 96:112 )B96 - 112
13X-RAY DIFFRACTION13( CHAIN C AND RESID 4:27 )C4 - 27
14X-RAY DIFFRACTION14( CHAIN C AND RESID 28:75 )C28 - 75
15X-RAY DIFFRACTION15( CHAIN C AND RESID 76:88 )C76 - 88
16X-RAY DIFFRACTION16( CHAIN C AND RESID 89:113 )C89 - 113
17X-RAY DIFFRACTION17( CHAIN D AND RESID 3:27 )D3 - 27
18X-RAY DIFFRACTION18( CHAIN D AND RESID 28:51 )D28 - 51
19X-RAY DIFFRACTION19( CHAIN D AND RESID 52:70 )D52 - 70
20X-RAY DIFFRACTION20( CHAIN D AND RESID 71:94 )D71 - 94
21X-RAY DIFFRACTION21( CHAIN D AND RESID 95:113 )D95 - 113

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