[English] 日本語
Yorodumi
- PDB-7vum: Crystal structure of SSB complexed with que -

+
Open data


ID or keywords:

Loading...

-
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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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
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

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)
12.2825-0.50733.54935.1112.0317.01940.26630.1226-0.1573-0.086-0.1448-0.066-0.1611-0.7766-0.06270.26030.01930.06280.29850.02560.24644.982-10.9-2.398
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more