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- PDB-3bzz: Crystal structural of the mutated R313T EscU/SpaS C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 3bzz
TitleCrystal structural of the mutated R313T EscU/SpaS C-terminal domain
Components(EscU) x 2
KeywordsMEMBRANE PROTEIN / PROTEIN TRANSPORT / Auto cleavage protein / Intein / flagella / 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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.407 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)15,4162
Polymers15,4162
Non-polymers00
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.297, 48.606, 62.464
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: 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: Q9AJ26
#2: Protein EscU


Mass: 9423.975 Da / Num. of mol.: 1 / Fragment: UNP residues 263-345 / Mutation: R313T
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.: 108 / 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: 1.54097 Å3/Da / Density % sol: 20.18 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.5
Details: (NH4)2SO4, Bis-Tris, Pentaerythriol Ethoxylate, NaCl, pH 6.5, 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: 1.407→50 Å / Num. all: 19177 / Num. obs: 18717 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.065 / Χ2: 1.264 / Net I/σ(I): 10.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.407-1.464.30.37815550.439183.3
1.46-1.525.20.33118220.473196.5
1.52-1.596.20.25418720.504199.6
1.59-1.677.10.21818900.551100
1.67-1.787.80.17818890.6111100
1.78-1.917.90.12918840.7961100
1.91-2.117.90.08419311.2031100
2.11-2.417.80.07919432.0451100
2.41-3.047.50.06919312.8071100
3.04-5070.0420002.21196.3

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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: 1.407→38.35 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.09 / SU ML: 0.041 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.219 959 5.1 %RANDOM
Rwork0.18 ---
all0.182 19177 --
obs0.182 18669 97.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.187 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20 Å20 Å2
2---0.28 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.407→38.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms786 0 0 108 894
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022815
X-RAY DIFFRACTIONr_bond_other_d0.0010.02542
X-RAY DIFFRACTIONr_angle_refined_deg1.4142.0021112
X-RAY DIFFRACTIONr_angle_other_deg0.93331357
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3135104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.5926.45231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.9215152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.613151
X-RAY DIFFRACTIONr_chiral_restr0.090.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02871
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02134
X-RAY DIFFRACTIONr_nbd_refined0.2260.2159
X-RAY DIFFRACTIONr_nbd_other0.1690.2543
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2409
X-RAY DIFFRACTIONr_nbtor_other0.0880.2404
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.268
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3190.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2080.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0830.217
X-RAY DIFFRACTIONr_mcbond_it1.0021.5698
X-RAY DIFFRACTIONr_mcbond_other0.2111.5202
X-RAY DIFFRACTIONr_mcangle_it1.1012838
X-RAY DIFFRACTIONr_scbond_it1.9923372
X-RAY DIFFRACTIONr_scangle_it2.414.5271
LS refinement shellResolution: 1.407→1.444 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 48 -
Rwork0.267 1082 -
all-1130 -
obs--80.14 %
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)
18.03481.64733.87839.85511.62112.9870.008-0.30470.53550.60480.07550.0967-0.7601-0.1965-0.08350.17980.04520.06610.06640.01220.1159-8.60284.024625.9362
23.4499-1.28271.68143.4578-1.41594.62080.0042-0.0199-0.1560.06960.11420.07070.12640.0217-0.11840.0853-0.00080.00760.02550.00720.0358-2.003-7.119121.0226
36.1885-4.024711.01135.5448-6.588319.7046-0.0252-0.2797-0.0907-0.08170.17270.156-0.2669-0.744-0.14750.07340.014-0.00260.10190.02820.024-11.15392.38218.0153
41.5597-0.11720.3881.3195-0.6045.0433-0.0457-0.1209-0.0150.08850.05770.0703-0.0296-0.0891-0.01210.1020.01120.00120.0364-0.00520.0648-4.7844-2.578923.1018
51.03080.046-0.03822.7678-0.75052.2683-0.03840.1278-0.039-0.2726-0.0014-0.10070.06650.0710.03990.0986-0.00350.00980.0328-0.00960.040.5622-5.733713.5866
650.44885.4008-6.610718.6084-9.004420.6582-0.02181.4485-2.5291-0.20930.05890.73321.2126-1.9318-0.03710.1784-0.1539-0.04860.2275-0.07320.1901-11.2361-11.549710.162
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A244 - 255
2X-RAY DIFFRACTION2A256 - 262
3X-RAY DIFFRACTION2B263 - 270
4X-RAY DIFFRACTION3B271 - 276
5X-RAY DIFFRACTION4B277 - 301
6X-RAY DIFFRACTION5B302 - 334
7X-RAY DIFFRACTION6B335 - 343

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