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- PDB-3bzx: Crystal structure of the mutated H265A EscU C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 3bzx
TitleCrystal structure of the mutated H265A EscU C-terminal domain
Components(EscURecea-Cristur) 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 / Resolution: 1.6 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 / Derived calculations / Category: 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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5013
Polymers15,4052
Non-polymers961
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 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)62,00312
Polymers61,6198
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 area13630 Å2
MethodPISA
3
A: EscU
B: EscU
hetero molecules

A: EscU
B: EscU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0026
Polymers30,8094
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area5560 Å2
MethodPISA
4
A: EscU
B: EscU
hetero molecules

A: EscU
B: EscU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0026
Polymers30,8094
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
Buried area5750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.739, 59.024, 72.132
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 / Recea-Cristur


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 / Recea-Cristur


Mass: 9412.995 Da / Num. of mol.: 1 / Fragment: UNP residues 263-345 / Mutation: H265A
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 / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 92 / 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: 1.93 Å3/Da / Density % sol: 36.12 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 8
Details: K2PO4 Peg3350, NaCl, Tris, pH 8.0, 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 / Date: May 29, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→45.69 Å / Num. all: 16060 / Num. obs: 15546 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.034 / Χ2: 1.277 / Net I/σ(I): 23
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.6660.23715620.955199.6
1.66-1.726.40.18815681.0411100
1.72-1.86.60.13315981.0441100
1.8-1.96.30.115811.435199.7
1.9-2.025.90.07514711.884192.2
2.02-2.1760.04814571.479190.8
2.17-2.396.60.03615291.259196.3
2.39-2.737.40.03216161.33199.9
2.73-3.447.60.02316151.01198.8
3.44-166.30.03215491.51190.7

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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: 1.6→16 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.765 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.219 768 4.9 %RANDOM
Rwork0.196 ---
all0.197 16060 --
obs0.197 15521 96.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.302 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20 Å2
2---0.56 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.6→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms789 0 5 92 886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.023898
X-RAY DIFFRACTIONr_bond_other_d0.0050.02604
X-RAY DIFFRACTIONr_angle_refined_deg1.5372.0161241
X-RAY DIFFRACTIONr_angle_other_deg0.95131523
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5755124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.98526.17634
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.63615175
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.204152
X-RAY DIFFRACTIONr_chiral_restr0.0930.2154
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02981
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02153
X-RAY DIFFRACTIONr_nbd_refined0.2170.2180
X-RAY DIFFRACTIONr_nbd_other0.1710.2608
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2452
X-RAY DIFFRACTIONr_nbtor_other0.0850.2459
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.261
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2970.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3260.216
X-RAY DIFFRACTIONr_mcbond_it0.9181.5749
X-RAY DIFFRACTIONr_mcbond_other0.2311.5216
X-RAY DIFFRACTIONr_mcangle_it1.0252922
X-RAY DIFFRACTIONr_scbond_it2.0563399
X-RAY DIFFRACTIONr_scangle_it2.8964.5308
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.488 66 -
Rwork0.436 1083 -
all-1149 -
obs--98.71 %
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)
113.03225.0638-5.337414.0748-5.072610.3657-0.28150.081-0.0994-1.0602-0.1184-0.68860.62520.26840.39990.14380.03560.02470.02980.05990.0707-13.7932-14.5187-21.0796
23.69031.27942.86565.57011.02614.2308-0.01940.04580.03440.0670.0282-0.0079-0.04740.11-0.00880.0771-0.0155-0.02570.03770.03020.0289-12.2693-19.9345-9.2308
32.18762.7181.043413.63422.14183.8139-0.14950.25810.0981-0.8492-0.08970.438-0.10170.20760.23920.1097-0.0021-0.03590.08980.02620.0546-12.487-24.2779-16.7641
42.411-1.42321.73353.9622-5.01686.3747-0.12750.14510.13070.56490.11940.1963-0.7084-0.03160.00810.1202-0.0179-0.01420.00990.02290.0036-15.396-15.5755-8.1925
54.41540.61520.44115.4782-1.462210.9956-0.02670.09240.09360.063-0.0367-0.47850.01340.62710.06340.0156-0.0086-0.00950.02860.01980.0548-4.3325-26.2026-9.0193
65.04590.5314-4.87186.0821-2.091812.04870.0310.1072-0.0909-0.2419-0.07570.02830.3610.16240.04470.06940.0009-0.00430.0314-0.01630.0281-11.0112-34.3402-11.4952
718.3585-7.66953.05539.6529-1.83622.2601-0.15-0.47960.02140.39660.21220.4998-0.1095-0.2453-0.06220.0297-0.0130.0164-0.0112-0.02710.0742-21.1256-29.5488-7.5838
817.6451.83277.53870.59621.58784.8166-0.64451.82790.2843-0.54830.2552-0.6718-0.06920.25530.38930.0598-0.06420.02440.11750.13030.2044-31.3336-23.197-14.4173
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A246 - 255
2X-RAY DIFFRACTION2A256 - 262
3X-RAY DIFFRACTION2B263 - 271
4X-RAY DIFFRACTION3B272 - 290
5X-RAY DIFFRACTION4B291 - 312
6X-RAY DIFFRACTION5B313 - 322
7X-RAY DIFFRACTION6B323 - 331
8X-RAY DIFFRACTION7B332 - 339
9X-RAY DIFFRACTION8B340 - 345

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