[English] 日本語
Yorodumi
- PDB-3seo: Crystal structure of VopL C terminal domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3seo
TitleCrystal structure of VopL C terminal domain
ComponentsVopL C terminal domain protein
KeywordsSTRUCTURAL PROTEIN / alpha helix
Function / homology
Function and homology information


actin binding / identical protein binding
Similarity search - Function
Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #170 / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1210 / : / : / VopL C-terminal dimerization domain / Wiskott Aldrich syndrome homology region 2 / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / WH2 motif / WH2 domain / WH2 domain profile. ...Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #170 / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1210 / : / : / VopL C-terminal dimerization domain / Wiskott Aldrich syndrome homology region 2 / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / WH2 motif / WH2 domain / WH2 domain profile. / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
WH2 domain-containing protein
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.305 Å
AuthorsYu, B. / Rosen, M.K. / Tomchick, D.R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Mechanism of actin filament nucleation by the bacterial effector VopL.
Authors: Yu, B. / Cheng, H.C. / Brautigam, C.A. / Tomchick, D.R. / Rosen, M.K.
History
DepositionJun 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VopL C terminal domain protein
B: VopL C terminal domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,97911
Polymers53,6602
Non-polymers3199
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-85 kcal/mol
Surface area25960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.180, 89.851, 103.007
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

-
Components

#1: Protein VopL C terminal domain protein


Mass: 26830.148 Da / Num. of mol.: 2 / Fragment: unp residues 247-484
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Gene: VopL, VPA1370 / Plasmid: pGEX2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q87GE5
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG1500, 100mM Tris pH=7.5, 100mM NaCl, 2mM TCEP, vapor diffusion, hanging drop, temperature 293K

-
Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 23092 / Num. obs: 23092 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.041 / Χ2: 1.051 / Net I/σ(I): 18.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.344.80.78511511.1199.7
2.34-2.385.10.7311351.029199.8
2.38-2.435.30.57311321.0311100
2.43-2.485.40.511331.0441100
2.48-2.535.40.41511531.0831100
2.53-2.595.40.31111351.0311100
2.59-2.665.40.26111571.0231100
2.66-2.735.40.2111590.9951100
2.73-2.815.40.14311341.0121100
2.81-2.95.40.11511740.9781100
2.9-35.40.0911391.0911100
3-3.125.40.06711541.1031100
3.12-3.265.40.05111531.1041100
3.26-3.445.30.03711791.102199.9
3.44-3.655.40.03111580.991100
3.65-3.935.30.0311731.134199.9
3.93-4.335.20.03311691.062199.8
4.33-4.955.10.03111901.0471100
4.95-6.244.90.02612141.054199.7
6.24-504.60.02611000.997185.2

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.2_432refinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
SOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.305→29.153 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8057 / SU ML: 0.4 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2748 1954 8.48 %RANDOM
Rwork0.2207 ---
all0.2254 23040 --
obs0.2254 23040 99.06 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 73.745 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso max: 257.74 Å2 / Biso mean: 88.6785 Å2 / Biso min: 34.11 Å2
Baniso -1Baniso -2Baniso -3
1-3.0994 Å2-0 Å2-0 Å2
2---1.9469 Å20 Å2
3----1.1525 Å2
Refinement stepCycle: LAST / Resolution: 2.305→29.153 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3501 0 9 36 3546
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033561
X-RAY DIFFRACTIONf_angle_d0.5644789
X-RAY DIFFRACTIONf_chiral_restr0.043533
X-RAY DIFFRACTIONf_plane_restr0.002625
X-RAY DIFFRACTIONf_dihedral_angle_d11.691325
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3049-2.38720.33481910.27622060225199
2.3872-2.48280.33011920.275320752267100
2.4828-2.59570.31621940.255320932287100
2.5957-2.73240.34071960.266821122308100
2.7324-2.90350.33951960.253321212317100
2.9035-3.12740.31261940.24520932287100
3.1274-3.44170.26791980.224121322330100
3.4417-3.93870.27741970.204921332330100
3.9387-4.95840.24722000.19521532353100
4.9584-29.15490.25491960.21962114231093
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)
13.5684-0.7309-1.53910.04450.21773.67480.26960.03660.7118-0.40040.0034-0.1348-0.29960.0272-0.17440.9874-0.0031-0.10960.3737-0.00120.43898.606639.176915.0529
22.03741.07732.16892.53150.1358.30230.3193-0.32510.27440.77360.844-0.3141-2.0911-0.537-0.22760.6001-0.0436-0.14020.4769-0.09270.5919.676636.989724.6369
36.9512-0.21823.91841.5796-1.40034.94891.12031.96810.3371-2.1534-0.00961.15551.46420.5746-0.77491.13240.075-0.32840.90450.00330.703932.377826.100647.8478
45.38032.70441.37013.43571.9062.6793-0.30180.32490.7541-0.28581.93971.30332.24815.4912-0.96920.78370.6296-0.45042.1762-0.30910.671233.42934.200548.2935
56.7015-0.27511.25711.88240.45823.42050.9121-1.8374-1.37050.4627-0.28210.16141.8419-0.0455-0.34071.1565-0.055-0.30220.80820.23480.935922.288229.549959.1187
61.05540.6316-0.458-0.2113-0.18063.2892-0.1526-0.1835-0.29170.08780.5529-0.18550.52620.6147-0.28070.51470.2499-0.2710.67820.01650.632124.09734.406344.3223
72.97032.44780.33532.3127-0.19220.77690.1374-0.8003-0.20250.2512-0.1351-0.01820.055-0.42130.04270.5150.0729-0.07530.4828-0.04230.43977.959925.364923.3758
8-0.60511.14410.54552.2081.71133.5431-0.15210.3153-0.0081-0.18650.2973-0.4842-0.22880.461-0.14820.479-0.04240.00310.4654-0.06410.487715.517724.39239.3764
94.17744.07951.00919.88040.96421.3944-0.16820.002-1.03520.94740.7667-1.5639-0.10530.1994-0.37850.7082-0.004-0.07260.66010.230.6755-4.5589-2.382717.5981
102.52970.4493-2.7964.1915-0.46732.7712-0.07230.9207-0.5746-0.33350.15560.8744-0.2967-0.766-0.27070.35880.0198-0.08810.55380.25080.622-21.52472.210716.1778
111.7311-0.1523-3.26161.53992.0186.65570.88590.32340.4516-0.0696-0.67830.0525-0.7238-2.0398-0.48540.59160.22910.19830.80630.38951.0067-37.42534.905731.8431
120.8512-0.34860.27954.15670.90290.7765-1.0218-0.0248-0.19010.26011.5369-1.15180.89081.0242-0.40690.9231-0.2701-0.0340.8189-0.07870.4943-30.53333.309943.1305
135.04051.7744-2.33810.4144-0.92881.94020.49420.2940.53710.06590.12130.2270.17080.3271-0.42930.38120.1044-0.03950.5570.19590.7225-28.91161.523427.9711
143.67652.3-1.29754.54020.10021.4114-0.0666-0.48450.40050.4950.13240.2243-0.0941-0.286-0.19950.4177-0.0356-0.04830.50570.13320.4098-9.85812.254116.861
151.41690.0502-0.35550.8619-0.31520.73-0.39240.11350.7233-0.44510.7560.7871-0.0887-0.8342-0.380.518-0.1598-0.19070.63990.28510.6254-15.343312.64625.4049
162.12681.7827-2.9431.7677-1.76443.807-0.06120.0721-0.2192-0.23420.34230.1546-0.122-0.2993-0.24970.4776-0.03740.02070.3781-0.07190.41043.10889.55813.0524
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 3:19)A3 - 19
2X-RAY DIFFRACTION2(chain A and resid 20:41)A20 - 41
3X-RAY DIFFRACTION3(chain A and resid 42:56)A42 - 56
4X-RAY DIFFRACTION4(chain A and resid 57:72)A57 - 72
5X-RAY DIFFRACTION5(chain A and resid 73:118)A73 - 118
6X-RAY DIFFRACTION6(chain A and resid 119:159)A119 - 159
7X-RAY DIFFRACTION7(chain A and resid 160:185)A160 - 185
8X-RAY DIFFRACTION8(chain A and resid 186:240)A186 - 240
9X-RAY DIFFRACTION9(chain B and resid 2:12)B2 - 12
10X-RAY DIFFRACTION10(chain B and resid 13:57)B13 - 57
11X-RAY DIFFRACTION11(chain B and resid 58:107)B58 - 107
12X-RAY DIFFRACTION12(chain B and resid 108:118)B108 - 118
13X-RAY DIFFRACTION13(chain B and resid 119:152)B119 - 152
14X-RAY DIFFRACTION14(chain B and resid 153:182)B153 - 182
15X-RAY DIFFRACTION15(chain B and resid 183:196)B183 - 196
16X-RAY DIFFRACTION16(chain B and resid 197:241)B197 - 241

+
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