[English] 日本語
Yorodumi
- PDB-8yli: Crystal structure of Pectobacterium atrosepticum PecS in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8yli
TitleCrystal structure of Pectobacterium atrosepticum PecS in complex with operator DNA
Components
  • (DNA (28-MER)) x 2
  • Regulatory protein
KeywordsTRANSCRIPTION / Transcription factor
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Regulatory protein
Similarity search - Component
Biological speciesPectobacterium atrosepticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSong, W.S. / Yoon, S.I.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)RS-2023-00208153 Korea, Republic Of
National Research Foundation (NRF, Korea)2022R1I1A1A01068105 Korea, Republic Of
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Structural basis of transcriptional regulation by UrtR in response to uric acid.
Authors: Song, W.S. / Ki, D.U. / Cho, H.Y. / Kwon, O.H. / Cho, H. / Yoon, S.I.
History
DepositionMar 6, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Regulatory protein
B: Regulatory protein
C: DNA (28-MER)
D: DNA (28-MER)


Theoretical massNumber of molelcules
Total (without water)55,3344
Polymers55,3344
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11680 Å2
ΔGint-92 kcal/mol
Surface area21950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.170, 80.504, 75.233
Angle α, β, γ (deg.)90.000, 93.482, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 15 through 21 or (resid 22...
d_2ens_1(chain "B" and ((resid 15 through 16 and (name N...

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: HIS / End label comp-ID: HIS / Auth seq-ID: 15 - 175 / Label seq-ID: 6 - 166

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (-0.0108909462793, 0.0539445833372, 0.998484536294), (0.0445790584138, -0.997524753909, 0.0543789747111), (0.998946492481, 0.045103738961, 0.00845918977535)Vector: -2. ...NCS oper: (Code: given
Matrix: (-0.0108909462793, 0.0539445833372, 0.998484536294), (0.0445790584138, -0.997524753909, 0.0543789747111), (0.998946492481, 0.045103738961, 0.00845918977535)
Vector: -2.26947689887, 19.249922158, 1.38368212556)

-
Components

#1: Protein Regulatory protein


Mass: 19064.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium atrosepticum (bacteria) / Gene: pecS, ECA2036 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6D5K4
#2: DNA chain DNA (28-MER)


Mass: 8568.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pectobacterium atrosepticum (bacteria)
#3: DNA chain DNA (28-MER)


Mass: 8635.629 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pectobacterium atrosepticum (bacteria)
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.89 Å3/Da / Density % sol: 68.36 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: sodium formate, sodium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 18873 / % possible obs: 99.2 % / Redundancy: 3 % / CC1/2: 0.992 / Net I/σ(I): 17.3
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 911 / CC1/2: 0.789 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8YLG

8ylg


Resolution: 2.9→27.46 Å / SU ML: 0.3124 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.6395
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2743 1072 5.76 %
Rwork0.2252 17523 -
obs0.2278 18595 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.12 Å2
Refinement stepCycle: LAST / Resolution: 2.9→27.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2330 1142 0 0 3472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00633646
X-RAY DIFFRACTIONf_angle_d0.83985193
X-RAY DIFFRACTIONf_chiral_restr0.0422615
X-RAY DIFFRACTIONf_plane_restr0.0067474
X-RAY DIFFRACTIONf_dihedral_angle_d23.92661375
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.339174897283 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.030.47081300.39212179X-RAY DIFFRACTION98.93
3.03-3.190.34211520.3562122X-RAY DIFFRACTION97.1
3.19-3.390.3671340.26122191X-RAY DIFFRACTION97.81
3.39-3.650.28961680.23812119X-RAY DIFFRACTION97.74
3.65-4.020.25231660.23742196X-RAY DIFFRACTION99.16
4.02-4.60.24361210.20552200X-RAY DIFFRACTION98.35
4.6-5.780.26661100.19632247X-RAY DIFFRACTION99.12
5.79-27.460.1804910.17022269X-RAY DIFFRACTION97.28
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)
11.36768674606-0.657126019871-1.04475296554.583284831521.250630762134.26029535437-0.1643757006960.01848594823260.4640498358670.7043414876910.531612953822-0.308643456405-0.1707335579270.191223431711-0.3552012320960.53898866923-0.009055096559370.1541129731440.342090674763-0.02555526697840.55473032342830.630827460919.095432575926.370693667
23.7843579998-0.338611795123-0.3963160524850.615116163352-0.2345759093047.82139589858-0.175225401095-0.0981014475945-0.270190559744-0.08202991766390.2376007371290.3121687539550.827679797994-0.547597460846-0.1006863465261.11058112889-0.1609233900970.619155820260.3153902789760.06246171214750.60986304844920.648464155-5.9673106241122.507027642
30.3670861647030.484113565644-0.1894236025772.2130029908-2.2386588752.61305250703-0.240333905066-0.0883487239162-0.516437817683-0.4563923190520.31013539276-0.344619748830.63152206206-0.1792262867880.3020995782961.11866732673-0.3231558477070.8202146190970.4198006753880.03554922962711.1277413828112.5077526385-5.9769244507928.857636424
42.48041588643-1.33874880410.9411052862991.30653656311-1.301659870861.53215123565-0.09603757603250.134017319659-0.2444597366390.849337177830.01220032513510.9660159981340.850775910506-0.3922154025150.06478472529130.87650845151-0.1666196474190.3714258824390.549314637348-0.1654495599940.78036512342617.9007060014-8.3060041046521.9378410851
53.06606165593-1.021293566572.161111804363.72504589496-0.531618918534.14521655368-0.123484716761-0.735017633219-0.05472616262391.060816976240.545843831464-0.4772059691890.17085780249-0.140964328361-0.4272044280191.322706580470.009986850762650.03775820240690.348309392794-0.1234183247950.54979705994431.27686123888.2379325025739.1674946805
60.6315256994370.906891773587-0.5399899938671.31385773695-0.7537138187990.676699085755-0.266677331544-0.137159713882-0.1947495496871.634077702590.05013441034040.6310250005390.363588768771-0.3036539951880.1543222370061.496995033450.00933583493050.4557783696130.487405219690.02229008164240.55564643426124.76125785793.1801320391233.0378066539
72.652308011840.01911768841710.03795072064172.301601092721.644095487745.1102381939-0.09386466140120.4086974125150.71737568377-0.3206660402090.130099068265-0.143519861463-1.15247869147-0.148802354946-0.1528860858680.6552956044030.06115248768660.2429245163890.4382056322980.0921042297350.44875309265220.695579548128.832489343113.8685751361
84.45080948345-2.723438767061.031059761966.35090130333-2.031982473313.01782478932-0.271883185091-0.1316482705260.2632478153551.452080155420.253435027635-0.546247544796-0.46831003126-0.3227520452210.014670436130.770703972210.05650407931850.05580296067680.348885697512-0.04034453981960.48707932238327.886781259122.119215551333.2968619752
91.840116764280.296034578610.2608936831850.238717224715-0.196247605853.044417244550.223215986699-0.223059021120.1283791400160.3630442730750.4538038104740.4835173584720.0719955258631-0.879816412855-0.1811369884961.28853585183-0.5701137432111.40597756261.141724616030.3231468368421.78202263486-6.91478062752-2.1236703177631.4222682725
103.624115882211.4313767883-3.059557836762.86761684361-3.253901327835.54820875652-0.2870441175380.707562417224-0.138405853679-1.382647743940.2755771023310.4953351687260.509115925711-0.0287534421140.1639520838671.66261904945-0.127713878310.7586006943720.9517285166190.0427701567290.685926488920.289060478618.25966125942.08952061106
110.2398286174540.304726398282-0.4605721144220.554814211845-1.218003801783.36012124124-0.2893027469450.549711036484-0.227354093672-0.2285327364970.139025815917-0.06902354107550.896270689409-0.2492128157180.4380069360511.6108995934-0.4096125774651.020900119191.179623128490.2511027241291.0350116870834.825831392823.0132906114-12.4629520356
120.391276711429-0.4184043227240.7917985563884.764639519230.2800636369234.03332566616-0.7834304104830.666563787651-0.480534537024-0.6676367921320.5175195980950.7966177634620.853382641428-1.110152787130.272632525730.990877652476-0.1747371496550.4628850305960.8833094511220.05257440095050.9735561954612.946676062613.36943793379.99630877899
131.976284641451.051245606270.1432957994780.714689800833-0.1529557140570.732627206645-0.1767538789640.1077134799330.150085263477-0.260134209970.4175060266580.1162022674730.0284561256903-0.329985674776-0.3433053713431.15287969251-0.4373234490561.01403560521.482375878770.08874583532952.10864068163-8.93745430895-5.2343991317432.8668082022
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 15 through 60 )AA15 - 601 - 46
22chain 'A' and (resid 61 through 76 )AA61 - 7647 - 62
33chain 'A' and (resid 77 through 94 )AA77 - 9463 - 80
44chain 'A' and (resid 95 through 152 )AA95 - 15281 - 138
55chain 'A' and (resid 153 through 175 )AA153 - 175139 - 161
66chain 'B' and (resid 14 through 60 )BB14 - 601 - 47
77chain 'B' and (resid 61 through 128 )BB61 - 12848 - 115
88chain 'B' and (resid 129 through 175 )BB129 - 175116 - 162
99chain 'C' and (resid 1 through 10 )CC1 - 10
1010chain 'C' and (resid 11 through 28 )CC11 - 28
1111chain 'D' and (resid 1 through 5 )DD1 - 5
1212chain 'D' and (resid 6 through 20 )DD6 - 20
1313chain 'D' and (resid 21 through 28 )DD21 - 28

+
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://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