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- PDB-3bzv: Crystal structural of the mutated T264A EscU C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 3bzv
TitleCrystal structural of the mutated T264A EscU C-terminal domain
Components(EscU) x 2
KeywordsMEMBRANE PROTEIN / PROTEIN TRANSPORT / Auto cleavage protein / Intein / T3SS
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
T3SS structure protein EscU / EscU
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.94 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)15,4422
Polymers15,4422
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.086, 52.086, 155.184
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein EscU


Mass: 5991.751 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: Q7DB59, UniProt: Q9AJ26*PLUS
#2: Protein EscU


Mass: 9450.039 Da / Num. of mol.: 1 / Fragment: UNP residues 263-345 / Mutation: T264A
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.: 31 / 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: 1.97 Å3/Da / Density % sol: 37.49 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 5.5
Details: Li2SO4, Bis-Tris, Peg3350, NaCl, pH 5.5, Microbatch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / 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: 1.94→50 Å / Num. all: 9981 / Num. obs: 9941 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13 % / Rmerge(I) obs: 0.066 / Χ2: 1.389 / Net I/σ(I): 10.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.94-2.0111.40.7259290.596197.4
2.01-2.0913.70.4679590.6761100
2.09-2.1813.70.3459750.74199.9
2.18-2.313.80.2289520.8451100
2.3-2.4413.60.1819760.8651100
2.44-2.6313.60.1259781.027199.6
2.63-2.913.50.0929991.27199.9
2.9-3.3213.30.0699961.778199.9
3.32-4.1812.30.06310323.184199.8
4.18-50110.05111452.936199.2

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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: 1.94→45.13 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 8.683 / SU ML: 0.124 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.268 474 4.8 %RANDOM
Rwork0.215 ---
all0.217 9981 --
obs0.217 9886 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.088 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å2-0.22 Å20 Å2
2---0.45 Å20 Å2
3---0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.94→45.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms825 0 0 31 856
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.022860
X-RAY DIFFRACTIONr_bond_other_d0.0030.02586
X-RAY DIFFRACTIONr_angle_refined_deg2.1081.9981169
X-RAY DIFFRACTIONr_angle_other_deg1.15331454
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.1955108
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.89224.70634
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.63615165
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.276154
X-RAY DIFFRACTIONr_chiral_restr0.1580.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02923
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02153
X-RAY DIFFRACTIONr_nbd_refined0.2450.2157
X-RAY DIFFRACTIONr_nbd_other0.1970.2567
X-RAY DIFFRACTIONr_nbtor_refined0.1850.2401
X-RAY DIFFRACTIONr_nbtor_other0.0980.2512
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2220.230
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1110.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.210.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2560.24
X-RAY DIFFRACTIONr_mcbond_it1.6281.5724
X-RAY DIFFRACTIONr_mcbond_other0.3551.5209
X-RAY DIFFRACTIONr_mcangle_it2.0062871
X-RAY DIFFRACTIONr_scbond_it2.7433395
X-RAY DIFFRACTIONr_scangle_it3.624.5296
LS refinement shellResolution: 1.94→1.992 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 31 -
Rwork0.245 672 -
all-703 -
obs--98.87 %
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)
110.96590.29621.156835.7439-9.78072.81610.0371-0.1699-0.4277-0.4231-0.2989-0.8408-0.1534-0.36420.261800.06220.0630.1913-0.06710.0465.069921.98962.8098
224.5239-3.0918-5.77936.8721-2.95025.44031.2883-0.2581-0.66440.4399-1.1958-1.5991.77240.1107-0.09260.10570.3267-0.0633-0.41340.0226-0.1878-3.63169.40424.7501
37.93320.30017.87153.86274.212325.5399-0.01430.3974-0.2980.14170.15220.00740.25110.2709-0.1379-0.27990.022-0.0132-0.1795-0.1162-0.2076-9.522516.1126-0.7592
41.7081.03050.61678.02126.279313.90480.02430.2478-0.22010.35370.1865-0.10520.15250.8402-0.2108-0.30640.0641-0.034-0.0719-0.1329-0.1642-3.60218.75772.8405
58.5489-0.8913-0.766714.0144-8.264127.22980.21110.4882-0.82431.14780.3856-0.21852.7616-0.0222-0.59670.00160.1094-0.0998-0.4614-0.191-0.1955-9.34216.0365-1.5478
67.15342.1931.39577.3302-0.63764.4896-0.0651.30520.1797-0.13950.32270.38930.11260.2422-0.2577-0.30860.0284-0.0116-0.0505-0.1361-0.2969-10.244420.7467-5.7045
79.97251.39770.30833.06562.93499.4648-0.15650.1680.3113-0.0698-0.05030.3908-0.6889-0.12870.2067-0.28860.0108-0.01-0.1865-0.1083-0.2037-9.001226.9042.6358
818.77944.85540.962530.01725.794624.6841-0.2185-1.5865-0.73662.55590.30391.76792.0354-0.9039-0.0854-0.0446-0.05790.2196-0.0208-0.1439-0.0711-19.118817.94589.0389
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A239 - 248
2X-RAY DIFFRACTION2A249 - 257
3X-RAY DIFFRACTION3A258 - 262
4X-RAY DIFFRACTION3B264 - 273
5X-RAY DIFFRACTION4B274 - 288
6X-RAY DIFFRACTION5B289 - 303
7X-RAY DIFFRACTION6B304 - 321
8X-RAY DIFFRACTION7B322 - 337
9X-RAY DIFFRACTION8B338 - 343

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