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- PDB-3bzs: Crystal structure of EscU C-terminal domain with N262D mutation, ... -

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Basic information

Entry
Database: PDB / ID: 3bzs
TitleCrystal structure of EscU C-terminal domain with N262D mutation, Space group P 21 21 21
ComponentsEscU
KeywordsMEMBRANE PROTEIN / PROTEIN TRANSPORT / Auto cleavage protein / intein / T3SS / TTSS / asparagine cyclization / membrane
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 / Resolution: 1.48 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 / 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


Theoretical massNumber of molelcules
Total (without water)15,4551
Polymers15,4551
Non-polymers00
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.371, 48.349, 60.630
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: 15454.796 Da / Num. of mol.: 1 / Fragment: C-terminal domain / Mutation: N262D
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 1.48 Å3/Da / Density % sol: 17.31 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.5
Details: PEG 3350, NaCl, Bis-Tris, pH 6.5, Microbatch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. all: 16014 / Num. obs: 14461 / % possible obs: 90.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.7 % / Rmerge(I) obs: 0.053 / Χ2: 1.573 / Net I/σ(I): 14.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.48-1.536.30.56712771.085182.7
1.53-1.598.40.45715621.234199
1.59-1.679.40.32615771.4121100
1.67-1.75100.24515761.5451100
1.75-1.8610.30.15815811.5661100
1.86-2.019.30.09911611.729173.5
2.01-2.21110.06716051.657199.8
2.21-2.5311.10.04911521.515172.2
2.53-3.1911.50.0416371.5271100
3.19-509.40.04513332.323176.6

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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: 1.48→37.8 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.666 / SU ML: 0.051 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.234 716 5 %RANDOM
Rwork0.215 ---
all0.216 16014 --
obs0.216 14388 90.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.043 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20 Å20 Å2
2---0.74 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.48→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms746 0 0 96 842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022780
X-RAY DIFFRACTIONr_bond_other_d0.0010.02532
X-RAY DIFFRACTIONr_angle_refined_deg1.6852.0051064
X-RAY DIFFRACTIONr_angle_other_deg1.51431329
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.73599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.87225.51729
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04315151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.975152
X-RAY DIFFRACTIONr_chiral_restr0.1840.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02826
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02132
X-RAY DIFFRACTIONr_nbd_refined0.2410.2132
X-RAY DIFFRACTIONr_nbd_other0.170.2527
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2390
X-RAY DIFFRACTIONr_nbtor_other0.0910.2406
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.256
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0850.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1280.214
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.29
X-RAY DIFFRACTIONr_mcbond_it1.0291.5660
X-RAY DIFFRACTIONr_mcbond_other0.2641.5187
X-RAY DIFFRACTIONr_mcangle_it1.132794
X-RAY DIFFRACTIONr_scbond_it2.0713366
X-RAY DIFFRACTIONr_scangle_it2.5724.5267
LS refinement shellResolution: 1.48→1.521 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.694 47 -
Rwork0.656 929 -
all-976 -
obs--84.21 %
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)
12.9295-0.9792-0.26143.31521.04483.10530.0258-0.094-0.17220.22270.1492-0.11750.20860.0565-0.17510.04350.013-0.0461-0.0005-0.00880.0355-9.42384.207-8.1722
21.4629-1.1066-2.00472.1882.03066.00180.0106-0.0435-0.0238-0.0780.1226-0.08460.12730.1492-0.13320.0369-0.0039-0.01510.0061-0.00870.0235-10.25960.3965-16.8657
36.5487-0.3346-0.57981.8814-0.45062.7353-0.0756-0.09460.0810.05980.17680.08920.0485-0.0817-0.10130.04410.0136-0.00380.05070.01710.0342-14.03295.1753-1.5502
44.7589-1.42352.57471.6304-1.70433.3894-0.12980.01590.14250.0314-0.0126-0.1224-0.18280.14410.14250.0425-0.0025-0.0207-0.0112-0.01280.0295-8.06939.8799-7.9703
52.2995-0.4328-0.93843.78270.75674.98850.12620.14160.044-0.2977-0.15470.2176-0.1137-0.19860.02850.02930.0027-0.0507-0.0004-0.00360.0267-17.88554.7628-19.6132
622.3532-1.753713.187310.5475-8.517220.26450.1550.47970.99810.1761-0.7534-0.4208-0.07831.97710.59840.0185-0.08240.030.15780.0630.0107-4.432210.5618-20.0053
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA248 - 26540 - 57
2X-RAY DIFFRACTION2AA266 - 28758 - 79
3X-RAY DIFFRACTION3AA288 - 29580 - 87
4X-RAY DIFFRACTION4AA296 - 31288 - 104
5X-RAY DIFFRACTION5AA313 - 335105 - 127
6X-RAY DIFFRACTION6AA336 - 341128 - 133

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