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- PDB-3c00: Crystal structural of the mutated G247T EscU/SpaS C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 3c00
TitleCrystal structural of the mutated G247T EscU/SpaS C-terminal domain
Components(EscU) x 2
KeywordsMEMBRANE PROTEIN / PROTEIN TRANSPORT / Auto cleavage protein / flagella / T3SS / Intein / Asparagine cyclization / YscU
Function / homology
Function and homology information


dioxygenase activity / protein secretion / isomerase activity / 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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.41 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 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EscU
B: EscU


Theoretical massNumber of molelcules
Total (without water)15,5162
Polymers15,5162
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.969, 53.884, 59.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein EscU


Mass: 6035.803 Da / Num. of mol.: 1 / Fragment: UNP residues 215-262
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: EPEC E2348/69 / Gene: escU / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9AJ26
#2: Protein EscU


Mass: 9480.065 Da / Num. of mol.: 1 / Fragment: UNP residues 263-345 / Mutation: G247T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: EPEC E2348/69 / Gene: escU / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9AJ26
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 1.4 Å3/Da / Density % sol: 12.08 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.5
Details: Tris, HEPES, Peg3350, NaCl, pH 7.5, Microbatch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
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: 1.41→50 Å / Num. all: 17245 / Num. obs: 17142 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12.9 % / Rmerge(I) obs: 0.057 / Χ2: 1.336 / Net I/σ(I): 11.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.41-1.478.30.69516740.443199.9
1.47-1.5311.70.56916890.4691100
1.53-1.613.60.38616940.5171100
1.6-1.6814.10.2617000.571100
1.68-1.7914.10.18316930.6281100
1.79-1.9314.10.11917160.8741100
1.93-2.12140.08717201.5871100
2.12-2.4313.70.0817312.6631100
2.43-3.0613.30.05317552.4861100
3.06-5012.30.03817702.723194.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.41→40 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.671 / SU ML: 0.051 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 867 5.1 %RANDOM
Rwork0.216 ---
all0.217 17245 --
obs0.217 17088 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.485 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2---0.23 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.41→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms814 0 0 45 859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022854
X-RAY DIFFRACTIONr_bond_other_d0.0040.02574
X-RAY DIFFRACTIONr_angle_refined_deg1.50321161
X-RAY DIFFRACTIONr_angle_other_deg0.96431428
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1345104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.32525.75833
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53715161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.129152
X-RAY DIFFRACTIONr_chiral_restr0.0850.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02909
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02145
X-RAY DIFFRACTIONr_nbd_refined0.2550.2151
X-RAY DIFFRACTIONr_nbd_other0.1780.2531
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2419
X-RAY DIFFRACTIONr_nbtor_other0.0860.2440
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1070.232
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.140.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2430.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.27
X-RAY DIFFRACTIONr_mcbond_it1.0671.5721
X-RAY DIFFRACTIONr_mcbond_other0.2591.5208
X-RAY DIFFRACTIONr_mcangle_it1.2122869
X-RAY DIFFRACTIONr_scbond_it1.953401
X-RAY DIFFRACTIONr_scangle_it2.3874.5292
LS refinement shellResolution: 1.41→1.451 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 43 -
Rwork0.299 1125 -
all-1168 -
obs--95.89 %
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)
12.5872-3.93115.370210.24140.946430.57570.0261-0.4486-0.3009-0.28630.0291.0901-0.409-2.423-0.05520.1885-0.046-0.02920.23690.05290.1076-11.84381.32625.3512
23.0164-0.51451.011714.83124.09645.19870.04290.282-0.1263-0.786-0.18850.5032-0.1670.17090.14560.03510.0062-0.02020.0546-0.01020.0741-3.2902-4.056612.0616
33.78620.77490.7155.69673.80759.4239-0.0082-0.15490.107-0.1019-0.04090.1373-0.1528-0.0950.04920.0402-0.0036-0.00110.06230.0050.0815-6.9297-3.639916.904
410.17956.00080.250711.5824-0.51538.5478-0.41750.6482-0.0428-0.91550.2771-0.28470.17350.45550.14040.161-0.04870.02170.12-0.00430.0166-1.9568-3.83444.1779
53.42832.8454-1.02557.1349-2.4413.80420.03240.1003-0.21470.007-0.0131-0.09110.21940.2495-0.01920.03650.0082-0.00990.0533-0.00750.0636-1.9222-10.446515.6533
66.522-0.6493.45716.6582-0.31826.21110.0643-0.346-0.22980.5962-0.10110.31270.4375-0.1840.03670.1435-0.04190.06450.10670.00850.068-7.3767-8.220125.0915
715.19239.0514-14.584410.0372-11.665817.87580.4404-0.22120.22140.4499-0.4322-0.4154-0.60530.2641-0.00820.0448-0.0165-0.02850.10960.01360.14267.0899-0.395619.7888
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A244 - 252
2X-RAY DIFFRACTION2A253 - 262
3X-RAY DIFFRACTION2B263 - 264
4X-RAY DIFFRACTION3B265 - 291
5X-RAY DIFFRACTION4B292 - 300
6X-RAY DIFFRACTION5B301 - 319
7X-RAY DIFFRACTION6B320 - 333
8X-RAY DIFFRACTION7B334 - 345

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