[English] 日本語
Yorodumi
- PDB-7tcb: Crystal Structure of the YaeQ Family Protein VPA0551 from Vibrio ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7tcb
TitleCrystal Structure of the YaeQ Family Protein VPA0551 from Vibrio parahaemolyticus
ComponentsYaeQ family protein VPA0551
KeywordsUNKNOWN FUNCTION / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyYaeQ / YaeQ superfamily / YaeQ protein / YaeQ / Restriction endonuclease type II-like / Uncharacterized protein
Function and homology information
Biological speciesVibrio parahaemolyticus RIMD 2210633 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsKim, Y. / Mulligan, R. / Maltseva, N. / Gu, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of the YaeQ Family Protein VPA0551 from Vibrio parahaemolyticus
Authors: Kim, Y. / Mulligan, R. / Maltseva, N. / Gu, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: YaeQ family protein VPA0551
B: YaeQ family protein VPA0551
C: YaeQ family protein VPA0551
D: YaeQ family protein VPA0551


Theoretical massNumber of molelcules
Total (without water)85,5014
Polymers85,5014
Non-polymers00
Water1629
1
A: YaeQ family protein VPA0551


Theoretical massNumber of molelcules
Total (without water)21,3751
Polymers21,3751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YaeQ family protein VPA0551


Theoretical massNumber of molelcules
Total (without water)21,3751
Polymers21,3751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: YaeQ family protein VPA0551


Theoretical massNumber of molelcules
Total (without water)21,3751
Polymers21,3751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: YaeQ family protein VPA0551


Theoretical massNumber of molelcules
Total (without water)21,3751
Polymers21,3751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.024, 47.687, 115.519
Angle α, β, γ (deg.)90.000, 99.720, 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

-
Components

#1: Protein
YaeQ family protein VPA0551


Mass: 21375.203 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus RIMD 2210633 (bacteria)
Strain: RIMD 2210633 / Gene: VPA0551 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Gold / References: UniProt: Q87IQ5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M sodium chloride, 0.1 M BIS-TRIS pH 6.5, 25 % (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 24176 / % possible obs: 95.1 % / Redundancy: 4.6 % / Biso Wilson estimate: 76.65 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.124 / Net I/σ(I): 15.5
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.799 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 844 / CC1/2: 0.621 / % possible all: 67.8

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→40.92 Å / SU ML: 0.4229 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.9873
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2647 1140 4.78 %
Rwork0.2235 22706 -
obs0.2253 23846 95.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.62 Å2
Refinement stepCycle: LAST / Resolution: 2.7→40.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5609 0 0 9 5618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00185747
X-RAY DIFFRACTIONf_angle_d0.43947790
X-RAY DIFFRACTIONf_chiral_restr0.0428868
X-RAY DIFFRACTIONf_plane_restr0.0035989
X-RAY DIFFRACTIONf_dihedral_angle_d13.88742138
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.820.38881100.35852232X-RAY DIFFRACTION75.06
2.82-2.970.3991350.33682652X-RAY DIFFRACTION90.31
2.97-3.160.3251590.30362895X-RAY DIFFRACTION99.22
3.16-3.40.31061630.27132934X-RAY DIFFRACTION99.84
3.4-3.740.27741320.2472964X-RAY DIFFRACTION99.9
3.74-4.280.28791520.21042971X-RAY DIFFRACTION99.84
4.29-5.40.22841370.18223001X-RAY DIFFRACTION100
5.4-40.920.22391520.20143057X-RAY DIFFRACTION98.62
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)
15.04161430374-0.931945769837-0.6181937744566.814068021012.691188094993.473314970750.0008766893598270.464419296223-0.5652048981810.923399568929-0.3090772837010.5603954467820.80914098435-0.381514791808-0.1175171683570.7342127189020.0407561927057-0.04021621450.5543088441370.03575164738060.705247466323-3.40259091241-7.6747447928993.6933940634
27.78798709382-1.941180098413.36431467030.540426415258-0.9406750273891.56764690483-0.1635865745371.55722145149-0.801478465718-0.452997234074-0.01776168179440.4954956730770.970497158865-0.46753554424-0.03682928107490.791666045076-0.104411965549-0.01195272776450.739230043296-0.08547367738730.716065983061-5.88207308924-5.9902071885783.1847979659
34.804382412042.0710614441-1.868803091355.49287621848-0.5892089877276.56284248404-0.1189633363770.543887132757-0.0422464702871-0.899546360760.05986981992950.7872435198840.169048692079-0.7732669362420.142839464870.875366097817-0.0309578413801-0.09554071139850.880739396125-0.05245000065720.57122315502-13.84531435580.56898936459878.8396530917
41.91687911651-2.103175629632.196904192374.36513253064-1.682788818995.29475273216-0.1002572509620.2706268345050.0819435695823-1.061603108820.0030490261353-0.2825630075670.3056516120950.4844968184930.1074697239640.733553568627-0.06869770853330.008368022378030.9473163002910.1549009217380.645393294188-0.685833007294.3797426619482.8939537904
54.497687435950.254394475482-2.727902143027.535765315613.431584434425.65048256496-0.601470052529-0.6312992547430.7233300746690.08434862404090.452086211615-0.772431220391-0.166791085086-0.221678145496-0.08382900168580.687603457432-0.06345514397170.0877712243950.8361054642910.01316785595680.3540442800120.6767082661095.8623668405991.1528363244
63.576294832440.3297791321955.016270276684.624504674640.2109205183567.632085839940.377355742759-1.68414050720.2340737499750.488555277863-0.124633893639-0.473380808914-0.546232187498-1.21794249112-0.2136143721690.6832653404550.05608254451510.2146313154081.39935228259-0.2149173197571.12969211289-13.3897103329-28.0247980108123.521009675
75.642044032581.72165469595-3.077412901762.9077891926-2.358638043815.419558187420.364922596488-0.1952458799521.02476363664-0.3852682307890.02048914705050.310758198089-0.51301170739-0.350410856807-0.2730118176880.6382220514340.1187269462830.06877071888450.586933607435-0.02828069755170.813683020673-8.08925384311-25.6497841818111.976784505
84.39980955464-0.89543484221-0.8774575762267.36583879544-2.718115196656.625097140520.202017409621.77300854212.37291255734-2.724750110970.864366936926-0.3173506490140.516747488327-0.360547575163-0.485587305180.7413078122470.09616651668190.2473101727130.673208652460.1779890381321.186283409532.0515224068-24.114683785100.95890558
94.64187737560.32990132856-0.2166634214524.76240323465-1.133850141477.084889282220.0538498916908-0.107247373946-0.0137765216402-0.0687071258759-0.17381332457-0.1344851641730.7641146294240.5312847120890.2518788663940.5920863017720.0413182079484-0.05509619247180.4539181808420.0013683711390.5568687667280.0229248639028-36.6410778417111.226624881
101.44534384206-0.927984250267-0.719639288433.703978405810.9514827762756.086961421990.168532426839-1.338549254850.1827951814040.830212853706-0.264125899960.6944393501750.342251505004-0.471751935630.1846963405630.9396127857-0.0723387688212-0.04176977571891.394951738820.01966597007980.684985133496-6.95289942966-36.8622030432124.673301334
113.430719328730.546376266944-1.452562706359.43011232285-1.334329275954.125546603390.5432463225280.346754039245-0.208367495215-1.84021792827-0.597367622125-0.669195615153-0.1285088287172.41150092022-0.02016069731141.15158112859-0.2145555821750.1348460576552.01982586870.04744254264430.66989554570525.59568790140.99330984603158.9538246731
121.669043260971.299024053891.213225352982.768154863374.279647154426.73407302363-0.02319727891890.2649943418560.53050710347-1.18958111850.233155037270.0732019362528-1.544623608511.6317310257-0.1535084822551.26642269181-0.1615619926510.007345638984641.673046678980.09195724480080.6090438273817.55533698662.779180157851.5179418329
133.289530458783.106970568581.309584489453.212251494220.2329207538923.336671440961.086888554210.725558243703-1.04134304918-1.28271947682-0.388685511131-0.560768781951-0.2278800123311.22041801586-0.1195622091111.46125517813-0.0181865544491-0.03120587417941.72698052734-0.09706944828090.42875194172616.0544186341-5.0837128059943.8510318321
143.174687044650.01915068633840.4302861902391.93654329619-0.4152995521491.88840256321-0.9810876043320.911435059238-0.278944983078-1.676404934710.8446799505610.975809320559-0.6121648859480.881376042665-0.04154679503981.24588116586-0.12490853534-0.13662277181.3543633258-0.221529740320.6269354594337.49395238801-4.1174273841546.6300308035
151.743395035951.347402927391.506263397824.608830158130.5487110680254.63772239910.06886776180780.07750856384660.430270182875-1.118669329770.1351653879520.755387209701-0.606757428515-0.059393110014-0.1563954936270.9764613107680.0231608893556-0.09988339652381.49953561926-0.1266817750950.7412778775610.462465154946-5.157067888352.4777081989
164.74348843229-0.3919706289841.695544413063.04807475877-1.802854811954.999893514230.194359798052-0.1026679705730.410091846170.149867713655-0.385580776870.0990957910018-0.9496233210610.4374518324940.1464653126680.828675950686-0.0171865830119-0.000673832418411.1867346102-0.02002997496210.48429514496616.02699645971.7853826857665.6030436151
176.56460536546-2.327303586151.404203864343.591818169720.05495367637664.49013667389-0.183031492893-0.1814218404080.1566985418190.484084154048-0.048932063593-0.409633330118-0.009652053457280.6687279045760.3035418406810.682428083285-0.1809589621630.04671830303321.399465354780.1444636438220.52995171961432.5281343083-11.144537100984.8715499571
186.814926306340.330660392519-0.01967935071733.58515255754-1.76610025569.991749202280.0723822922366-0.591934473254-0.1822744075371.064461830550.0445119692193-0.569635005366-1.113912690750.895791119368-0.2003078154360.716227186745-0.0204993657344-0.05924418841890.9701793574330.008384061298110.58875418100523.515275707-14.744249162598.310386779
192.91142104272-0.5720556697340.2675832643014.63417720106-3.351071045786.213655136840.1403898889270.585411003775-0.176196690914-0.496069147492-0.253326867014-0.01593034436660.3903415755581.474092172860.1818871347370.6913040574740.0582489743188-0.03318663793361.08604570997-0.05871451737310.54919040126223.8904844043-20.560681249583.3644402568
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 4 through 31 )CC4 - 311 - 28
22chain 'C' and (resid 32 through 68 )CC32 - 6829 - 62
33chain 'C' and (resid 69 through 110 )CC69 - 11063 - 104
44chain 'C' and (resid 111 through 155 )CC111 - 155105 - 149
55chain 'C' and (resid 156 through 179 )CC156 - 179150 - 173
66chain 'D' and (resid 3 through 31 )DD3 - 311 - 29
77chain 'D' and (resid 32 through 88 )DD32 - 8830 - 82
88chain 'D' and (resid 89 through 98 )DD89 - 9883 - 92
99chain 'D' and (resid 99 through 142 )DD99 - 14293 - 136
1010chain 'D' and (resid 143 through 178 )DD143 - 178137 - 172
1111chain 'A' and (resid 4 through 31 )AA4 - 311 - 28
1212chain 'A' and (resid 32 through 68 )AA32 - 6829 - 61
1313chain 'A' and (resid 69 through 88 )AA69 - 8862 - 81
1414chain 'A' and (resid 89 through 110 )AA89 - 11082 - 103
1515chain 'A' and (resid 111 through 133 )AA111 - 133104 - 126
1616chain 'A' and (resid 134 through 178 )AA134 - 178127 - 171
1717chain 'B' and (resid 3 through 49 )BB3 - 491 - 47
1818chain 'B' and (resid 50 through 98 )BB50 - 9848 - 93
1919chain 'B' and (resid 99 through 181 )BB99 - 18194 - 176

+
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