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- PDB-3bzp: Crystal structural of the mutated N262A EscU C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 3bzp
TitleCrystal structural of the mutated N262A EscU C-terminal domain
ComponentsEscU
KeywordsMEMBRANE PROTEIN / PROTEIN TRANSPORT / Intein / T3SS / membrane / asparagine cyclization
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: 1.499 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)15,4111
Polymers15,4111
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: EscU

A: EscU

A: EscU

A: EscU


Theoretical massNumber of molelcules
Total (without water)61,6434
Polymers61,6434
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation4_545x,-y-1,-z1
crystal symmetry operation3_455-x-1,y,-z1
Buried area3930 Å2
MethodPISA
3
A: EscU

A: EscU


Theoretical massNumber of molelcules
Total (without water)30,8222
Polymers30,8222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
Buried area1290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.535, 59.169, 71.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-399-

HOH

21A-400-

HOH

31A-404-

HOH

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Components

#1: Protein EscU


Mass: 15410.784 Da / Num. of mol.: 1 / Fragment: C-terminal domain / Mutation: N262A
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.: 69 / 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: 1.95 Å3/Da / Density % sol: 36.98 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 5.5
Details: Citrate, PEG 6000, t-Butanol, 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: 0.97956 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: 0.97956 Å / Relative weight: 1
ReflectionResolution: 1.499→50 Å / Num. all: 19754 / Num. obs: 18747 / % possible obs: 94.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.051 / Χ2: 1.561 / Net I/σ(I): 12.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.499-1.555.80.417720.483190.4
1.55-1.626.80.32118980.517198.3
1.62-1.697.60.2419490.571100
1.69-1.787.70.17219520.6681100
1.78-1.897.60.11719520.898199.8
1.89-2.046.70.09619291.622198.1
2.04-2.247.30.07217882.071191.5
2.24-2.5670.0717933.164189.9
2.56-3.237.20.05219943.2591100
3.23-506.50.03517202.545181.9

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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: 1.499→45.69 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.62 / SU ML: 0.048 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.213 962 5.1 %RANDOM
Rwork0.194 ---
all0.19456 19754 --
obs0.19456 18744 94.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.565 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20 Å20 Å2
2---1.05 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.499→45.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms790 0 0 69 859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022850
X-RAY DIFFRACTIONr_bond_other_d0.0010.02566
X-RAY DIFFRACTIONr_angle_refined_deg1.6342.0051168
X-RAY DIFFRACTIONr_angle_other_deg1.09231417
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6285113
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.2525.62532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.67215157
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.264152
X-RAY DIFFRACTIONr_chiral_restr0.3360.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02937
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02149
X-RAY DIFFRACTIONr_nbd_refined0.2350.2165
X-RAY DIFFRACTIONr_nbd_other0.1710.2575
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2440
X-RAY DIFFRACTIONr_nbtor_other0.0870.2460
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.235
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.120.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2950.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.210
X-RAY DIFFRACTIONr_mcbond_it1.2151.5721
X-RAY DIFFRACTIONr_mcbond_other0.2261.5207
X-RAY DIFFRACTIONr_mcangle_it1.2422879
X-RAY DIFFRACTIONr_scbond_it2.3563395
X-RAY DIFFRACTIONr_scangle_it3.0564.5285
LS refinement shellResolution: 1.499→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 59 -
Rwork0.274 1219 -
all-1278 -
obs--88.75 %
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)
11.2322-0.78370.22477.8469-2.76450.97630.10550.05380.1377-0.215-0.1844-0.06320.09160.04340.07890.0842-0.01360.03580.07070.02360.094-14.9476-16.9441-15.2818
22.12060.29390.73259.76121.02313.5310.07950.18110.0732-0.1919-0.24970.03140.02920.26680.17020.0775-0.01040.01510.1160.02110.0855-13.0352-24.285-14.8914
31.6006-1.32830.63266.0041-3.37113.272-0.00110.08640.16380.7375-0.0562-0.016-0.54510.15460.05730.1592-0.06210.01040.05590.01040.0423-14.8929-15.0827-8.4592
41.73360.0367-0.87667.7225-0.30643.91320.09180.10730.05240.1305-0.2164-0.650.10320.48840.12450.0294-0.00360.00750.12570.03140.0955-7.3411-29.7053-10.5213
512.1149-8.70042.349711.4897-4.35631.9893-0.1149-0.35280.00360.2980.27250.65490.0912-0.19-0.15760.0718-0.02830.0520.0396-0.04410.1504-21.4024-29.8778-7.7002
621.7575-0.06218.90275.2431-1.08177.8463-0.5131.83440.259-0.62840.209-1.0981-0.28640.60020.3040.1472-0.12140.01950.08480.03230.1794-32.7853-23.5187-14.8863
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA246 - 26338 - 55
2X-RAY DIFFRACTION2AA264 - 28756 - 79
3X-RAY DIFFRACTION3AA288 - 31280 - 104
4X-RAY DIFFRACTION4AA313 - 330105 - 122
5X-RAY DIFFRACTION5AA331 - 340123 - 132
6X-RAY DIFFRACTION6AA341 - 345133 - 137

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