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- PDB-4ftf: Structure of the Type II secretion system pilotin AspS from Vibri... -

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Basic information

Entry
Database: PDB / ID: 4ftf
TitleStructure of the Type II secretion system pilotin AspS from Vibrio cholerae
ComponentsAlternate secretin pathway subunit S (VC395_1821, VC1703)
KeywordsPROTEIN TRANSPORT / pilotin / lipoprotein / secretin / protein secretion / PfamB PB000779 / secretin binding / outer membrane
Function / homologyGMP Synthetase; Chain A, domain 3 - #250 / Type II secretion system (T2SS) pilotin, S protein / Type II secretion system (T2SS) pilotin, S protein / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / metal ion binding / Alpha Beta / ACETATE ION / Lipoprotein
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.48 Å
AuthorsKorotkov, K.V. / Evans, T.J.
CitationJournal: Plos Pathog. / Year: 2013
Title: Assembly of the Type II Secretion System such as Found in Vibrio cholerae Depends on the Novel Pilotin AspS.
Authors: Dunstan, R.A. / Heinz, E. / Wijeyewickrema, L.C. / Pike, R.N. / Purcell, A.W. / Evans, T.J. / Praszkier, J. / Robins-Browne, R.M. / Strugnell, R.A. / Korotkov, K.V. / Lithgow, T.
History
DepositionJun 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Alternate secretin pathway subunit S (VC395_1821, VC1703)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6337
Polymers12,2601
Non-polymers3736
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.160, 63.860, 47.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Alternate secretin pathway subunit S (VC395_1821, VC1703)


Mass: 12259.997 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 55-163
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: 569B / Gene: VC395_1821, VC_1703 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q9KRD9
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.11 Å3/Da / Density % sol: 41.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M ZINC ACETATE, 20% PEG 3350, pH 7.5, vapor diffusion, hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.48→47.54 Å / Num. all: 17954 / Num. obs: 17689 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.123 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 16.17
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.48-1.520.9581.439662207484.8
1.52-1.560.7432.0312066225693.3
1.56-1.610.5892.9915382234599.1
1.61-1.650.5293.7170512253100
1.65-1.710.4114.82170512241100
1.71-1.770.3276.03164372155100
1.77-1.840.2428.19156502052100
1.84-1.910.18510.8151811988100
1.91-20.14313.81145681898100
2-2.090.11816.91139631819100
2.09-2.210.08921.25131211705100
2.21-2.340.07723.81129611679100
2.34-2.50.06626.78117781527100
2.5-2.70.0628.86109911424100
2.7-2.960.05333.85101901321100
2.96-3.310.04239.3290451186100
3.31-3.820.03644.8279721053100
3.82-4.680.03348.976690885100
4.68-6.620.03346.415300698100
6.620.0348.962729371100

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHARPphasing
SOLOMONphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.48→47.54 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.1765 / WRfactor Rwork: 0.155 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.9095 / SU B: 1.996 / SU ML: 0.041 / SU R Cruickshank DPI: 0.0671 / SU Rfree: 0.0664 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1765 907 5.1 %RANDOM
Rwork0.155 ---
all0.1561 17954 --
obs0.1561 17689 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 50.64 Å2 / Biso mean: 17.1693 Å2 / Biso min: 7.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2--0.59 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.48→47.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms830 0 15 169 1014
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.019870
X-RAY DIFFRACTIONr_bond_other_d0.0030.02592
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.9921174
X-RAY DIFFRACTIONr_angle_other_deg0.8833.0031457
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2165116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.225.26338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.62915169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.35157
X-RAY DIFFRACTIONr_chiral_restr0.0910.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02972
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02155
LS refinement shellResolution: 1.48→1.519 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 37 -
Rwork0.232 982 -
all-1019 -
obs--84.92 %
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)
112.3079-2.46750.7557.41350.5095.33060.16360.4466-0.37820.0256-0.1427-0.02650.10250.1977-0.02090.0364-0.0033-0.00920.111-0.02370.015434.51613.6912.879
22.8422-0.9352-0.47063.60282.73827.4785-0.00330.0182-0.07950.046-0.020.05640.06330.11980.02320.02630.0008-0.00040.0691-0.01080.017830.51117.97619.699
31.8801-1.2469-2.30693.81973.95718.8922-0.022-0.11560.01290.0329-0.10940.1062-0.0463-0.21070.13140.02650.00080.0010.0701-0.01620.039724.22523.76630.265
43.7791-11.31056.127633.8833-18.02613.0452-0.0308-0.0717-0.24040.11890.18650.74170.2211-0.3409-0.15580.0696-0.0436-0.0030.10390.02270.090326.36922.21541.432
53.6687-1.58631.116314.3227-8.284811.63750.0516-0.3791-0.18390.4248-0.04860.0756-0.25470.0333-0.00310.0212-0.0102-0.00610.07860.010.02231.11623.68242.605
63.0375-2.3417-3.91173.46026.344511.73650.07720.00040.1144-0.24140.107-0.1103-0.47430.2235-0.18420.0785-0.0194-0.0080.05020.00980.0434.64624.70326.867
76.9094-1.8459-3.77745.31198.063920.0840.1399-0.31510.0401-0.2396-0.0003-0.1748-0.43460.282-0.13960.0393-0.0061-0.00690.04850.00050.036734.98724.57134.086
82.0854-0.10363.50882.1475-5.718620.2859-0.0367-0.06810.03430.17540.04970.0294-0.4732-0.2714-0.01290.07470.00210.00980.1001-0.01080.017636.98524.99752.554
95.33940.6272.15666.12520.630913.5987-0.0479-0.1650.05440.0991-0.1241-0.22840.0675-0.01140.17210.05380.0117-0.01030.07280.02720.023141.97617.11348.316
1016.621212.00687.713312.99365.353910.7830.3141-0.2824-0.62110.3347-0.1092-0.51940.24360.0984-0.2050.06040.0166-0.00660.07540.02530.028437.85713.14441.863
118.3373-2.02113.93713.35792.612211.23770.1491-0.3393-0.40060.08170.07820.1041-0.0313-0.4294-0.22730.0614-0.01290.02040.0670.03430.060429.78810.16736.638
124.42560.5993-1.98111.9717-1.546.1834-0.03340.0334-0.1488-0.1058-0.00250.07520.0705-0.18220.03590.0424-0.004-0.00320.0381-0.0120.03931.20110.26128.487
133.23983.17145.65676.12258.068312.0855-0.05840.0708-0.0666-0.07780.1981-0.0327-0.09260.3137-0.13970.04780.0197-0.0060.0992-0.02870.056938.1720.44333.304
148.1289-2.5575-6.973719.02181.22497.62090.1784-0.1230.45480.31910.0654-0.665-0.43580.2751-0.24380.0697-0.0026-0.02570.0959-0.00870.059141.38831.11644.223
153.16581.50915.246113.876512.798416.7540.03470.0423-0.0192-0.02030.1379-0.18560.03160.1729-0.17250.0259-0.00340.01410.1041-0.00560.030942.56419.79836.145
1613.29140.9742-4.29158.8633-5.211821.071-0.07540.0033-0.8602-0.0605-0.0602-0.17640.5980.31840.13560.05170.0229-0.00850.03210.00280.07640.3277.77131.226
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 10
2X-RAY DIFFRACTION2A11 - 17
3X-RAY DIFFRACTION3A18 - 27
4X-RAY DIFFRACTION4A28 - 31
5X-RAY DIFFRACTION5A32 - 37
6X-RAY DIFFRACTION6A38 - 45
7X-RAY DIFFRACTION7A46 - 50
8X-RAY DIFFRACTION8A51 - 59
9X-RAY DIFFRACTION9A60 - 65
10X-RAY DIFFRACTION10A66 - 71
11X-RAY DIFFRACTION11A72 - 77
12X-RAY DIFFRACTION12A78 - 87
13X-RAY DIFFRACTION13A88 - 93
14X-RAY DIFFRACTION14A94 - 100
15X-RAY DIFFRACTION15A101 - 106
16X-RAY DIFFRACTION16A107 - 111

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