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- PDB-3bzo: Crystal structural of native EscU C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 3bzo
TitleCrystal structural of native 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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 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 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EscU
B: EscU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5683
Polymers15,4722
Non-polymers961
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
MethodPISA
2
A: EscU
B: EscU
hetero molecules

A: EscU
B: EscU
hetero molecules

A: EscU
B: EscU
hetero molecules

A: EscU
B: EscU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,27212
Polymers61,8878
Non-polymers3844
Water1448
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 area13790 Å2
MethodPISA
3
A: EscU
B: EscU
hetero molecules

A: EscU
B: EscU
hetero molecules

A: EscU
B: EscU
hetero molecules

A: EscU
B: EscU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,27212
Polymers61,8878
Non-polymers3844
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
Buried area12520 Å2
MethodPISA
4
A: EscU
B: EscU
hetero molecules

A: EscU
B: EscU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1366
Polymers30,9444
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area5590 Å2
MethodPISA
5
A: EscU
B: EscU
hetero molecules

A: EscU
B: EscU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1366
Polymers30,9444
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area5860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.692, 58.708, 72.605
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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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: 9480.065 Da / Num. of mol.: 1 / Fragment: UNP residues 263-345
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 1.92 Å3/Da / Density % sol: 35.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: K2SO4, PEG 3350, pH 8.0, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 30, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 19563 / Num. obs: 19133 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.8 % / Rmerge(I) obs: 0.047 / Χ2: 1.316 / Net I/σ(I): 16.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.5-1.5510.70.53818661.094195.7
1.55-1.6211.90.38518821.134199.2
1.62-1.6912.20.27519311.141199.1
1.69-1.7812.30.20119101.166199.5
1.78-1.8912.30.12519291.255199.6
1.89-2.0411.20.09518321.858193.8
2.04-2.24120.05718931.441197.8
2.24-2.5611.50.04718631.512195.1
2.56-3.2312.20.0419821.3571100
3.23-5011.40.03220451.252198.2

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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: 1.5→45.64 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.916 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.225 979 5.2 %RANDOM
Rwork0.202 ---
all0.203 19563 --
obs0.203 19002 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.242 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20 Å20 Å2
2---1.21 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.5→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms787 0 5 86 878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022865
X-RAY DIFFRACTIONr_bond_other_d0.0070.02580
X-RAY DIFFRACTIONr_angle_refined_deg1.2892.011190
X-RAY DIFFRACTIONr_angle_other_deg0.81431458
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1835117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.85225.88234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.84215168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.083152
X-RAY DIFFRACTIONr_chiral_restr0.0730.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02941
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02149
X-RAY DIFFRACTIONr_nbd_refined0.5030.3188
X-RAY DIFFRACTIONr_nbd_other0.3240.3616
X-RAY DIFFRACTIONr_nbtor_refined0.2080.5447
X-RAY DIFFRACTIONr_nbtor_other0.1420.5421
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.594
X-RAY DIFFRACTIONr_metal_ion_refined0.780.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3640.312
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3790.333
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.523
X-RAY DIFFRACTIONr_mcbond_it0.8522529
X-RAY DIFFRACTIONr_mcbond_other0.2412206
X-RAY DIFFRACTIONr_mcangle_it1.3973878
X-RAY DIFFRACTIONr_scbond_it1.1692342
X-RAY DIFFRACTIONr_scangle_it1.8233303
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 60 -
Rwork0.253 1307 -
all-1367 -
obs--98.06 %
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)
11.2256-0.06720.9443.2321-1.20812.24470.00190.03860.1373-0.2423-0.0484-0.02930.11890.04210.04650.08970.01640.00440.05410.02560.1019-14.4628-16.8875-15.9461
210.84067.97610.395911.69589.055513.10230.0747-0.0036-0.08110.1408-0.0376-0.12070.02320.1489-0.03710.0272-0.016-0.00290.02410.02380.0275-11.2418-21.0789-10.4001
323.0509-25.995416.294142.47-8.056619.61280.0044-0.3628-0.9136-3.3742-0.35582.047-0.3625-0.82510.35140.30720.0421-0.23310.0792-0.05780.1771-19.5641-30.519-22.6971
40.87011.59621.26469.32432.52323.076-0.02410.1013-0.04650.07350.0361-0.5384-0.23240.4051-0.0120.0408-0.0404-0.02810.05110.03450.0461-8.3647-19.0837-13.2401
51.6072-1.5481.68994.4466-4.83266.059-0.10040.00790.13040.52420.11450.2409-0.5982-0.0212-0.0140.0733-0.0060.00330.00140.01830.0281-16.3273-14.8285-8.5435
62.45030.7991-0.21164.44370.71955.1873-0.01220.1010.03290.02960.0275-0.2780.00020.2912-0.01530.02630.01770.00970.03240.00930.0513-6.8823-28.9836-10.3533
711.2451-3.81721.74041.4197-0.71560.395-0.13780.17540.372-0.14350.12950.01710.0069-0.07790.00830.0706-0.02240.00040.0280.01140.123-24.0857-28.1847-9.9655
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA246 - 26238 - 54
2X-RAY DIFFRACTION2BB264 - 2722 - 10
3X-RAY DIFFRACTION3BB273 - 27811 - 16
4X-RAY DIFFRACTION4BB279 - 29217 - 30
5X-RAY DIFFRACTION5BB293 - 31031 - 48
6X-RAY DIFFRACTION6BB311 - 32949 - 67
7X-RAY DIFFRACTION7BB330 - 34568 - 83

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