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- PDB-6w08: Crystal Structure of Motility Associated Killing Factor E from Vi... -

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Basic information

Entry
Database: PDB / ID: 6w08
TitleCrystal Structure of Motility Associated Killing Factor E from Vibrio cholerae
ComponentsMotility Associated Killing Factor E
KeywordsTOXIN / Tripartite pore forming toxin / Cytotoxin / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologymembrane / ACETIC ACID / FORMIC ACID / : / Non-hemolytic enterotoxin lytic component L1
Function and homology information
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsKim, Y. / Jedrzejczak, R. / Joachimiak, G. / Endres, 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: J.Bacteriol. / Year: 2022
Title: A Genomic Island of Vibrio cholerae Encodes a Three-Component Cytotoxin with Monomer and Protomer Forms Structurally Similar to Alpha-Pore-Forming Toxins.
Authors: Herrera, A. / Kim, Y. / Chen, J. / Jedrzejczak, R. / Shukla, S. / Maltseva, N. / Joachimiak, G. / Welk, L. / Wiersum, G. / Jaroszewski, L. / Godzik, A. / Joachimiak, A. / Satchell, K.J.F.
History
DepositionFeb 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_symmetry
Revision 1.2Apr 3, 2024Group: 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: Motility Associated Killing Factor E
B: Motility Associated Killing Factor E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,14511
Polymers79,6552
Non-polymers4919
Water5,819323
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.209, 45.134, 143.950
Angle α, β, γ (deg.)90.000, 100.157, 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

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Motility Associated Killing Factor E


Mass: 39827.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_A0884 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KL63

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Non-polymers , 6 types, 332 molecules

#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Potassium thiocyanate 0.1M Bis Tris propane pH 6.5 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 74404 / % possible obs: 98 % / Redundancy: 4.1 % / Biso Wilson estimate: 30.39 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 15.8
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.053 / Num. unique obs: 3667 / CC1/2: 0.466 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: the same protein structure from SAD phasing with a lower resolution.

Resolution: 1.75→49.49 Å / SU ML: 0.2106 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.6169
RfactorNum. reflection% reflection
Rfree0.1965 3656 4.94 %
Rwork0.1745 --
obs0.1756 74012 97.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 40.53 Å2
Refinement stepCycle: LAST / Resolution: 1.75→49.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5556 0 13 323 5892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00325743
X-RAY DIFFRACTIONf_angle_d0.53287820
X-RAY DIFFRACTIONf_chiral_restr0.0379937
X-RAY DIFFRACTIONf_plane_restr0.00261032
X-RAY DIFFRACTIONf_dihedral_angle_d14.37653501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.770.35451120.31472424X-RAY DIFFRACTION87.21
1.77-1.80.26791060.29562663X-RAY DIFFRACTION94.09
1.8-1.820.30961270.2742593X-RAY DIFFRACTION95.2
1.82-1.850.27711290.25662679X-RAY DIFFRACTION96.73
1.85-1.880.29341420.22692697X-RAY DIFFRACTION97.76
1.88-1.910.22131460.21422698X-RAY DIFFRACTION97.77
1.91-1.940.2421430.20122679X-RAY DIFFRACTION97.78
1.94-1.980.25121500.20482699X-RAY DIFFRACTION97.87
1.98-2.020.22741340.19162698X-RAY DIFFRACTION98.03
2.02-2.060.24011400.19142646X-RAY DIFFRACTION95.02
2.06-2.10.23041320.18632649X-RAY DIFFRACTION97.41
2.1-2.150.20791720.17362733X-RAY DIFFRACTION98.24
2.15-2.210.21161500.15792701X-RAY DIFFRACTION98.21
2.21-2.270.16991460.15882725X-RAY DIFFRACTION98.32
2.27-2.330.22411480.16292686X-RAY DIFFRACTION98.27
2.33-2.410.19361110.16812776X-RAY DIFFRACTION98.63
2.41-2.490.24221350.17252769X-RAY DIFFRACTION98.64
2.49-2.590.23991380.17752706X-RAY DIFFRACTION98.41
2.59-2.710.19061290.17662677X-RAY DIFFRACTION96
2.71-2.850.21291620.17272751X-RAY DIFFRACTION98.91
2.85-3.030.20461470.18242753X-RAY DIFFRACTION99.38
3.03-3.270.21441370.17882817X-RAY DIFFRACTION99.49
3.27-3.60.18321390.17212780X-RAY DIFFRACTION99.25
3.6-4.120.18361760.14982696X-RAY DIFFRACTION96.77
4.12-5.180.14221750.14642776X-RAY DIFFRACTION99.43
5.18-49.490.18011300.17972885X-RAY DIFFRACTION97.54
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)
13.764956330482.510552493682.550483061193.45968489132.428534600523.43505862973-0.04901153760660.1660570773710.0776616541729-0.123618523336-0.04945581594880.00840506082771-0.0229041651197-0.102311580967-0.05863407053240.2225705884820.05781569990970.003750519061280.2893946468590.02805132782910.1799775892968.607764668074.8656094489921.9706272005
25.523650787931.487739665272.122565879251.698590737670.8940093652513.098902892810.2191067834910.0631001420390.591306852030.208097009678-0.2809969162150.1334270211490.101118527475-0.1191435871880.1375521529220.2405702983540.05942097059590.008381019450110.2381149162590.02747192996060.2619960308919.3467003518718.06888423830.3073291874
33.389695390471.364409026711.633441086861.706993065971.19055784551.64220411508-0.1509143657990.2494431257320.00630753095358-0.296793336026-0.07873721554730.2293739534490.015219104934-0.3313064073760.2603771108780.30728144515-0.001920296111410.002985367413260.525417544060.0006737851926740.261562492733-7.516418119962.0371195221812.7640564367
48.686352489045.887272693591.915401825346.830051297391.152402555472.50048259213-0.4155696245661.19235083870.384820872042-0.4931101196610.4596661196170.204709969311-0.1175830882510.225169315935-0.03171320216210.2332770202420.03528052849140.01379492183960.4393748875550.06071897695720.20277481143127.46475025469.8414620077421.3461935099
50.942332760832-0.615857786995-0.7393288821970.818920724251-0.3547509732042.21783240232-0.03491623632620.71968958439-0.764926960595-0.2449216331770.2569420299-0.3793802424860.392434486424-0.107097923770.1079919276950.3089682570720.00154708756934-0.01102510780680.336955932489-0.1008690771780.31254496947313.3877146094-3.2974059471626.5368980843
64.363149215843.193112330422.853471717352.919266015882.936417512393.029509220440.149741465399-0.101688475276-0.04914302581240.193264516621-0.11648631339-0.06127953574260.205462983521-0.195471405011-0.08512985922110.260707268198-0.0171339638857-0.01116523971720.2902444057560.02769923640130.24809891554320.96737232675.7205263626433.4221602513
74.458991384072.569625106442.061429032243.389817714321.742361946071.978656952240.1003261251980.435713136045-0.2528997982050.07967050289560.134355850673-0.4034399971060.144374774060.240696992973-0.236181586450.1950334374620.04591809191250.008518375587140.2667038366570.005290548847910.22555281144430.71236968177.3690348569229.9153046422
87.825125288874.438609732615.197191995383.726197472953.526199088044.52897904749-0.4207178361060.7068339733940.0335307014626-0.5155367977660.1998547725920.197777292509-0.2897409363630.04197672996850.2447012187790.3671154987670.0107843829128-0.003718185191030.553986637262-0.004593575130230.266932551590.476335832854.348958200789.83445631471
96.022392591642.225310718234.784914839223.334931503381.791247651045.769071600420.1280184788310.369907696241-0.766308332755-0.172246084558-0.19936191264-0.08430802198670.916818568598-0.1720523115180.04909268310140.484887349679-0.100461745360.04289731759380.605385904096-0.1331634935270.43289205673-11.5598267315-13.58644466486.4750999977
100.9987468620460.2280141361672.286872799871.812141115960.4681766178535.67189866740.754722038222-0.3319511669-1.101819264260.53263910668-0.208868878981-0.7174843493980.1964648629370.210433733897-0.3216737212750.350043855620.0293200634019-0.0789971965540.2591220064690.007587258909810.40320949609420.2506766241-0.89521791498935.4668696079
112.5934139896-2.574736768511.408110514144.56351810215-1.944700758911.455990470070.02412779531230.05270055508530.0348878704448-0.0632173505173-0.073126587344-0.1302771562960.1006063666420.1097521302560.03768824815950.226060320880.003213178586010.02349301217380.209529265-0.01938665903920.15654555645518.0845050185-0.41590527079451.5735838
125.94466793894-5.184240013012.43085043645.99438478373-2.125453608521.20598713578-0.402646841778-0.2396454027530.3240484025910.5497636039040.193755506273-0.464612351078-0.1659618433210.01566744526850.2384197723580.2512271767970.003197680494970.009815952240020.2131122680650.001349552158540.18019350141220.21312923494.2553885246859.2776563581
132.97279398688-0.691015382961-1.047969690251.147933533830.6178881098552.03781934134-0.131444080202-0.16406327545-0.1646493710430.1818326096980.06016676837250.05731688347820.254075731537-0.003958028540140.05084848549760.258646075578-0.0357041535695-0.003045436832180.1893528550280.008922831519120.225943952529-3.025473373071.8566207457749.2022981386
142.79340542475-1.734342275011.315593820221.98455313512-0.818319408650.89932887494-0.0612687559396-0.207043598772-0.05395704812050.08661699344650.06373574734810.04968337133830.0820326688575-0.101331806066-0.01568254146870.196052537106-0.01204285500260.04385326385710.1733497237380.02339272003330.1479628107383.535813298022.2068359445150.804911883
153.61243887152-2.186249322212.57055505383.18831540331-1.553006830323.425272565190.352123104399-0.0367447101719-0.506771683306-0.146996295902-0.01140183810870.266937091960.5072733380440.129541644984-0.2999494073840.234614261283-0.004226340466170.02546471554980.161028176881-0.00740616583050.24102535780419.1627870713-14.18417317453.6954305431
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 41 )
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 70 )
3X-RAY DIFFRACTION3chain 'A' and (resid 71 through 159 )
4X-RAY DIFFRACTION4chain 'A' and (resid 160 through 190 )
5X-RAY DIFFRACTION5chain 'A' and (resid 191 through 208 )
6X-RAY DIFFRACTION6chain 'A' and (resid 209 through 230 )
7X-RAY DIFFRACTION7chain 'A' and (resid 231 through 264 )
8X-RAY DIFFRACTION8chain 'A' and (resid 265 through 309 )
9X-RAY DIFFRACTION9chain 'A' and (resid 310 through 341 )
10X-RAY DIFFRACTION10chain 'A' and (resid 342 through 358 )
11X-RAY DIFFRACTION11chain 'B' and (resid 2 through 103 )
12X-RAY DIFFRACTION12chain 'B' and (resid 104 through 159 )
13X-RAY DIFFRACTION13chain 'B' and (resid 160 through 208 )
14X-RAY DIFFRACTION14chain 'B' and (resid 209 through 309 )
15X-RAY DIFFRACTION15chain 'B' and (resid 310 through 357 )

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