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- PDB-3c03: Crystal structure of the EscU C-terminal domain with P263A mutati... -

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Basic information

Entry
Database: PDB / ID: 3c03
TitleCrystal structure of the EscU C-terminal domain with P263A mutation,space group P 1 21 1
Components(EscU) x 3
KeywordsMEMBRANE PROTEIN / PROTEIN TRANSPORT / Auto cleavage protein / intein succinimid / Asparagine cyclization / 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: 1.9 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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id
Revision 2.1Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EscU
B: EscU
C: EscU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9714
Polymers30,8563
Non-polymers1151
Water1,13563
1
A: EscU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5432
Polymers15,4281
Non-polymers1151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: EscU
C: EscU


Theoretical massNumber of molelcules
Total (without water)15,4282
Polymers15,4282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.111, 55.478, 50.448
Angle α, β, γ (deg.)90.000, 108.690, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein EscU


Mass: 15427.772 Da / Num. of mol.: 1 / Fragment: UNP residues 215-345 / Mutation: P263A
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: 5973.736 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
#3: Protein EscU


Mass: 9454.028 Da / Num. of mol.: 1 / Fragment: UNP residues 263-345 / Mutation: P263A
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
#4: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2 / Details: Proline amino acid
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsASN went under reaction of cyclization to form succinimid intermediate

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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: 1.55 Å3/Da / Density % sol: 20.67 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.5
Details: Proline, HEPES, Peg3350, NaCl, pH 7.5, 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: Apr 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97956 Å / Relative weight: 1
ReflectionResolution: 1.9→47.78 Å / Num. all: 14927 / Num. obs: 14569 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.066 / Χ2: 1.909 / Net I/σ(I): 14.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.974.90.54713580.568192.6
1.97-2.056.30.40714300.618196.2
2.05-2.146.90.27914590.811197.6
2.14-2.257.30.19514551.014198
2.25-2.397.30.15614501.176197.8
2.39-2.587.40.11914651.478198.6
2.58-2.837.20.09114682.121198.5
2.83-3.2470.07314763.199198.9
3.24-4.076.50.05814904.053199.2
4.07-166.30.04515183.673198.8

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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: 1.9→16 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.971 / SU ML: 0.115 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.239 731 5 %RANDOM
Rwork0.173 ---
all0.176 14927 --
obs0.176 14554 97.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.045 Å2
Baniso -1Baniso -2Baniso -3
1-1.89 Å20 Å2-0.29 Å2
2---1.57 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.9→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1536 0 8 63 1607
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221600
X-RAY DIFFRACTIONr_bond_other_d0.0040.021074
X-RAY DIFFRACTIONr_angle_refined_deg1.7842.012177
X-RAY DIFFRACTIONr_angle_other_deg1.02732676
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5145200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.6525.73861
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1915294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.03154
X-RAY DIFFRACTIONr_chiral_restr0.1090.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021714
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02271
X-RAY DIFFRACTIONr_nbd_refined0.2750.3315
X-RAY DIFFRACTIONr_nbd_other0.2070.31034
X-RAY DIFFRACTIONr_nbtor_refined0.1880.5765
X-RAY DIFFRACTIONr_nbtor_other0.0970.5836
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.595
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1170.38
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2310.319
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.512
X-RAY DIFFRACTIONr_mcbond_it1.69421345
X-RAY DIFFRACTIONr_mcbond_other0.3792393
X-RAY DIFFRACTIONr_mcangle_it1.98631628
X-RAY DIFFRACTIONr_scbond_it1.4572730
X-RAY DIFFRACTIONr_scangle_it2.0283546
LS refinement shellResolution: 1.9→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 54 -
Rwork0.229 928 -
all-982 -
obs--90.67 %
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)
10.95712.12450.45226.9541-1.9614.14140.0970.0209-0.13790.49910.01550.21630.0188-0.1951-0.11250.18360.00470.04740.0857-0.00160.1299-10.7861-15.91532.4858
28.0126-5.04864.24086.0017-4.33674.8956-0.1531-0.106-0.20060.08570.24520.1083-0.1535-0.1936-0.09210.13480.012-0.01220.109-0.00810.1492-12.6364-8.2404-2.1938
31.5286-0.29741.309912.0146-4.59148.4808-0.1995-0.2178-0.08950.9222-0.1507-0.4091-0.11510.22840.35020.16610.0033-0.02490.14450.01180.1133-5.1352-15.59627.1749
45.90820.41311.182415.2807-4.105722.0822-0.08540.1116-0.3986-0.14410.2878-0.01051.1201-0.0921-0.20250.2523-0.0970.04460.0380.01840.1425-12.4118-23.63732.1346
52.76840.97790.07295.9879-2.03185.906-0.18750.01970.1323-0.0859-0.0116-0.6272-0.39960.42320.19910.1055-0.064-0.01610.0822-0.02460.1694-3.2995-6.56-3.2435
630.952221.68256.506545.66698.8574.1198-0.76371.4459-0.3603-1.74591.2347-0.18020.10030.1356-0.4710.2697-0.0934-0.01210.1279-0.05390.0593-10.7213-14.5584-12.5415
71.542-2.8848-1.724412.0452-8.93224.16140.55510.18411.55980.6869-1.29320.6040.1876-0.34030.73810.17570.05610.09880.05850.01620.28110.922212.780315.6699
88.774-0.99491.92551.6240.35698.83520.16570.1043-0.3067-0.5331-0.0258-0.1623-0.6608-0.0711-0.13990.35020.0599-0.00630.0587-0.0130.0164-1.24592.17119.688
91.4182-0.5641-0.97781.7398-0.51646.04670.12680.01680.0445-0.1507-0.0561-0.0854-0.3896-0.3321-0.07070.22770.05840.01010.14370.02970.0722-0.58733.224621.3338
106.22220.05640.3582.9884-1.386712.63390.0706-0.183-0.2942-0.19480.19640.3070.2258-1.9233-0.2670.073-0.0505-0.04440.30380.07460.0425-9.0034-2.172126.6936
1146.0174-17.7491-14.393413.0015-2.278514.46210.3996-0.2016-0.7502-2.0421-0.70031.04861.2101-0.38140.30070.3618-0.0252-0.09290.09250.0350.1396-1.4899-8.54828.4429
1254.42562.5668-11.758812.140424.055670.75180.5398-0.8728-2.1052-1.1459-1.3871-1.79763.4292.2540.84730.4120.37550.13680.11470.15080.16546.1835-10.260625.0008
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A247 - 264
2X-RAY DIFFRACTION2A265 - 281
3X-RAY DIFFRACTION3A282 - 295
4X-RAY DIFFRACTION4A296 - 303
5X-RAY DIFFRACTION5A304 - 334
6X-RAY DIFFRACTION6A335 - 343
7X-RAY DIFFRACTION7B245 - 251
8X-RAY DIFFRACTION8C264 - 266
9X-RAY DIFFRACTION8B252 - 261
10X-RAY DIFFRACTION9C267 - 303
11X-RAY DIFFRACTION10C304 - 331
12X-RAY DIFFRACTION11C332 - 337
13X-RAY DIFFRACTION12C338 - 343

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