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- PDB-3seo: Crystal structure of VopL C terminal domain -

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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 / WH2 motif / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / 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 / WH2 motif / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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.

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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 / Chloride


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


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

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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: 2.38 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

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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

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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

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