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- PDB-3c01: Crystal structural of native SpaS C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 3c01
TitleCrystal structural of native SpaS C-terminal domain
Components(Surface presentation of antigens protein ...) x 2
KeywordsMEMBRANE PROTEIN / PROTEIN TRANSPORT / Auto cleavage protein / flagella / EscU / YscU / Intein / T3SS / membrane / Inner membrane / Transmembrane / Virulence
Function / homology
Function and homology information


protein secretion / : / membrane => GO:0016020 / plasma membrane
Similarity search - Function
secretion proteins EscU / name from scop / Type III exporter system, secretion apparatus protein BsaZ / Type III secretion system substrate exporter / Type III secretion system substrate exporter, C-terminal / FlhB HrpN YscU SpaS Family / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CYSTEINE / Surface presentation of antigens protein SpaS
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsZarivach, R. / Deng, W. / Vuckovic, M. / Felise, H.B. / Nguyen, H.V. / Miller, S.I. / Finlay, B.B. / Strynadka, N.C.J.
CitationJournal: Nature / Year: 2008
Title: Structural analysis of the essential self-cleaving type III secretion proteins EscU and SpaS.
Authors: Zarivach, R. / Deng, W. / Vuckovic, M. / Felise, H.B. / Nguyen, H.V. / Miller, S.I. / Finlay, B.B. / Strynadka, N.C.
History
DepositionJan 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jan 22, 2020Group: Advisory / Derived calculations
Category: database_PDB_caveat / pdbx_struct_assembly ...database_PDB_caveat / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.4Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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: Surface presentation of antigens protein spaS
E: Surface presentation of antigens protein spaS
B: Surface presentation of antigens protein spaS
F: Surface presentation of antigens protein spaS
C: Surface presentation of antigens protein spaS
G: Surface presentation of antigens protein spaS
D: Surface presentation of antigens protein spaS
H: Surface presentation of antigens protein spaS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,38618
Polymers68,3038
Non-polymers1,08310
Water64936
1
A: Surface presentation of antigens protein spaS
E: Surface presentation of antigens protein spaS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2934
Polymers17,0762
Non-polymers2172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-13 kcal/mol
Surface area6520 Å2
MethodPISA
2
B: Surface presentation of antigens protein spaS
F: Surface presentation of antigens protein spaS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2934
Polymers17,0762
Non-polymers2172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-14 kcal/mol
Surface area6770 Å2
MethodPISA
3
C: Surface presentation of antigens protein spaS
G: Surface presentation of antigens protein spaS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4115
Polymers17,0762
Non-polymers3353
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-12 kcal/mol
Surface area6580 Å2
MethodPISA
4
D: Surface presentation of antigens protein spaS
H: Surface presentation of antigens protein spaS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3895
Polymers17,0762
Non-polymers3133
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-12 kcal/mol
Surface area6620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.663, 96.663, 217.511
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11G
21E
31F
41G

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 5 / Auth seq-ID: 269 - 276 / Label seq-ID: 11 - 18

Dom-IDAuth asym-IDLabel asym-ID
1GF
2EB
3FD
4GF

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Components

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Surface presentation of antigens protein ... , 2 types, 8 molecules ABCDEFGH

#1: Protein/peptide
Surface presentation of antigens protein spaS


Mass: 5708.480 Da / Num. of mol.: 4 / Fragment: UNP residues 211-258
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: EPEC E2348/69 / Gene: spaS / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P40702
#2: Protein
Surface presentation of antigens protein spaS


Mass: 11367.178 Da / Num. of mol.: 4 / Fragment: UNP residues 259-356
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: EPEC E2348/69 / Gene: spaS / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P40702

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Non-polymers , 4 types, 46 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CYS / CYSTEINE / Cysteine


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7NO2S
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: 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: 4.29 Å3/Da / Density % sol: 71.36 %
Crystal growTemperature: 293 K / pH: 8
Details: (NH4)SO4, MPD, L-Cystein, NaCl, Tris, pH 8.0, vapor diffusion, temperature 293K, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→83.62 Å / Num. obs: 36776 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.2
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.733 / % possible all: 98.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.6→83.62 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.925 / SU B: 14.774 / SU ML: 0.154 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.246 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1831 5 %RANDOM
Rwork0.223 ---
obs0.225 34839 99.4 %-
all-36924 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å2-0.35 Å20 Å2
2---0.7 Å20 Å2
3---1.04 Å2
Refinement stepCycle: LAST / Resolution: 2.6→83.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3445 0 61 36 3542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223562
X-RAY DIFFRACTIONr_bond_other_d0.0020.022421
X-RAY DIFFRACTIONr_angle_refined_deg1.8341.9984828
X-RAY DIFFRACTIONr_angle_other_deg1.18935935
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9745423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.59224.103156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.96715665
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1731528
X-RAY DIFFRACTIONr_chiral_restr0.2110.2579
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023775
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02657
X-RAY DIFFRACTIONr_nbd_refined0.2350.2724
X-RAY DIFFRACTIONr_nbd_other0.2030.22375
X-RAY DIFFRACTIONr_nbtor_refined0.190.21719
X-RAY DIFFRACTIONr_nbtor_other0.0980.22025
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.293
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0120.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3030.211
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9471.52752
X-RAY DIFFRACTIONr_mcbond_other0.1491.5856
X-RAY DIFFRACTIONr_mcangle_it1.13923541
X-RAY DIFFRACTIONr_scbond_it1.97531582
X-RAY DIFFRACTIONr_scangle_it3.1194.51285
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
C45medium positional0.190.5
A45medium positional0.20.5
B45medium positional0.190.5
D45medium positional0.240.5
C71loose positional0.735
A71loose positional0.855
B71loose positional1.045
D71loose positional0.95
C45medium thermal0.592
A45medium thermal1.062
B45medium thermal0.532
D45medium thermal0.482
C71loose thermal0.7610
A71loose thermal1.4810
B71loose thermal0.8710
D71loose thermal1.2310
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 146 -
Rwork0.405 2462 -
obs--97.28 %
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)
158.9925-8.91415.61777.0284-11.328518.29210.25991.2515-2.5571-1.83780.38470.40871.33760.998-0.64450.3907-0.0546-0.02940.3531-0.06470.432116.6951-52.408925.529
26.08620.8611.25224.13632.53365.60070.0797-0.29-0.01380.3180.0289-0.1705-0.06080.1836-0.10860.1457-0.10030.04560.41810.01520.336115.6958-39.987133.1597
32.78911.5389-0.52843.40272.19433.5045-0.12480.38120.1389-0.21830.26370.11340.1142-0.0597-0.13890.1794-0.067-0.00750.41280.030.395712.9828-41.835527.8424
47.4215-1.0137-0.88264.0546-1.26973.36590.06370.20570.7281-0.02720.1554-0.0987-0.1895-0.2328-0.21920.1933-0.08870.04020.3669-0.05250.310613.9122-34.082928.7482
516.91630.7455-8.46265.85850.76519.27680.41350.05481.2066-0.08620.2574-0.1781-1.1505-0.5543-0.67090.2517-0.03990.03230.3328-0.1410.419213.237-28.125937.8543
629.78168.8405-26.411235.4366-10.591248.8806-0.2074-1.7526-1.58370.0106-0.0113-0.91731.29570.8780.21870.001-0.0381-0.09730.75910.01290.4017.1049-37.395150.6345
7138.6204-26.388-26.854118.4317-11.558725.92882.99076.64651.2829-3.8768-1.18621.0621-1.3762-1.167-1.80460.82450.0083-0.23750.74510.39390.5578-6.9602-25.990624.6155
86.6163-2.2364-1.31966.7016-1.74954.5555-0.15890.29630.14290.17260.0196-0.05710.2286-0.03260.13930.15360.0099-0.01140.4273-0.05940.3086-8.0995-35.221237.0312
95.5471-0.18780.54962.5964-1.18636.90990.05440.62510.67760.0545-0.0964-0.0507-0.3016-0.31360.04210.10460.06260.05270.47740.03590.3844-11.3162-30.218234.8688
105.5069-0.24530.82153.29160.63384.18170.0027-0.09440.65420.28070.00240.0867-0.2281-0.2279-0.00520.18970.01360.08190.3318-0.00920.409-11.629-31.27743.0921
1112.890810.951811.679110.09668.593312.8108-0.208-0.3330.380.6446-0.10011.00410.2048-0.21070.30810.22890.0750.03950.4312-0.01940.3222-12.7693-41.575247.5193
1210.30670.454219.148246.39351.580335.5859-0.16980.6954-2.1406-0.96450.0874-2.3861.12671.7080.08240.19840.09070.18310.5859-0.21370.6433-14.6211-53.457737.6879
1368.29647.3566-14.792923.9165-4.872125.98781.66812.5382.1157-0.69060.1517-1.3367-1.31420.4554-1.81980.6843-0.35890.33230.3045-0.2390.615426.6233-57.8635-10.3521
147.52773.1173-2.0377.11271.17645.4533-0.29660.1296-0.3148-0.50470.2942-0.04620.0278-0.30380.00250.4105-0.19550.06510.232-0.02080.338121.4606-53.26671.6864
152.61371.1249-2.0877.4670.29785.1512-0.49270.2461-0.2332-0.49310.4995-0.91890.18950.0013-0.00680.3959-0.33440.10.2442-0.13970.410626.8638-52.8609-1.1922
162.65153.23412.39.071-1.551710.4054-0.2323-0.19640.10280.5839-0.1755-1.29870.18930.0480.40780.3525-0.11640.07050.1784-0.02290.41828.6156-51.08178.7719
173.0322-2.6119-1.66929.82545.32326.2379-0.3259-0.34460.17340.44810.7126-0.78550.43930.3225-0.38670.417-0.17050.03050.297-0.06120.373321.2244-55.553612.0805
1818.1485-19.4084-3.333545.5823-6.56547.11130.05460.05860.0688-1.76360.60331.47340.9185-1.0398-0.65790.404-0.2472-0.01560.32180.07260.345812.1138-38.80276.4609
195.289-1.0815-0.658912.2689-2.79668.42810.2592-0.0353-0.13220.1421-0.1401-0.71320.02320.5656-0.11910.2818-0.23740.07550.3091-0.05160.319734.5482-32.66749.1317
2013.08457.776912.80518.62486.811919.1488-0.05690.30870.2193-0.56060.0510.5875-0.3239-0.18410.00590.419-0.15870.14360.2773-0.04690.309126.4684-30.05845.3717
2111.3147-1.314-0.18763.8461-1.76052.76560.5508-0.8836-0.03630.2194-0.2587-0.3355-0.299-0.0234-0.29220.4028-0.24790.08740.2532-0.07650.343833.6218-29.12911.4067
224.9411.8371-2.05635.0533-0.3844.70990.3804-0.25050.51080.4892-0.12750.2342-0.66020.217-0.25280.4402-0.26840.13850.2507-0.06230.350929.4564-23.561910.8129
233.5553.4859-1.251910.5799-1.83838.24470.3236-0.03540.81820.59890.49741.1002-0.9931-0.4328-0.8210.2495-0.08080.12950.28240.08340.471620.7734-23.98924.8744
2432.8622-1.1912-12.455624.697511.904634.1213-1.08682.3949-0.4982-1.95451.1958-0.9631.7516-0.6081-0.1090.7962-0.40460.14350.3549-0.09080.29931.302-23.9521-10.5273
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A239 - 244
2X-RAY DIFFRACTION2A245 - 258
3X-RAY DIFFRACTION2E261 - 273
4X-RAY DIFFRACTION3E274 - 295
5X-RAY DIFFRACTION4E296 - 323
6X-RAY DIFFRACTION5E324 - 336
7X-RAY DIFFRACTION6E337 - 346
8X-RAY DIFFRACTION7B239 - 243
9X-RAY DIFFRACTION8B244 - 258
10X-RAY DIFFRACTION8F261 - 273
11X-RAY DIFFRACTION9F274 - 295
12X-RAY DIFFRACTION10F296 - 324
13X-RAY DIFFRACTION11F325 - 336
14X-RAY DIFFRACTION12F337 - 345
15X-RAY DIFFRACTION13C240 - 244
16X-RAY DIFFRACTION14C245 - 258
17X-RAY DIFFRACTION14G259 - 273
18X-RAY DIFFRACTION15G274 - 297
19X-RAY DIFFRACTION16G298 - 315
20X-RAY DIFFRACTION17G316 - 334
21X-RAY DIFFRACTION18G335 - 345
22X-RAY DIFFRACTION19H259
23X-RAY DIFFRACTION19D240 - 258
24X-RAY DIFFRACTION20H260 - 273
25X-RAY DIFFRACTION21H274 - 295
26X-RAY DIFFRACTION22H296 - 317
27X-RAY DIFFRACTION23H318 - 335
28X-RAY DIFFRACTION24H336 - 345

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