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- PDB-3sze: Crystal structure of the passenger domain of the E. coli autotran... -

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Basic information

Entry
Database: PDB / ID: 3sze
TitleCrystal structure of the passenger domain of the E. coli autotransporter EspP
ComponentsSerine protease espP
KeywordsHYDROLASE / parallel beta-helix / serine protease
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / cell outer membrane / periplasmic space / serine-type endopeptidase activity / cell surface / proteolysis / extracellular region
Similarity search - Function
Pectate Lyase C-like - #20 / Peptidase S6, IgA endopeptidase / Peptidase family S6 domain / Immunoglobulin A1 protease / Peptidase family S6 domain profile. / Autotransporter beta-domain / Outer membrane autotransporter barrel / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain ...Pectate Lyase C-like - #20 / Peptidase S6, IgA endopeptidase / Peptidase family S6 domain / Immunoglobulin A1 protease / Peptidase family S6 domain profile. / Autotransporter beta-domain / Outer membrane autotransporter barrel / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain / Autotransporter beta-domain superfamily / Autotransporter, pectate lyase C-like domain superfamily / Thrombin, subunit H - #120 / Pectate Lyase C-like / Pectin lyase fold/virulence factor / 3 Solenoid / Thrombin, subunit H / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Serine protease EspP
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsKhan, S. / Mian, H.S. / Sandercock, L.E. / Battaile, K.P. / Lam, R. / Chirgadze, N.Y. / Pai, E.F.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Crystal Structure of the Passenger Domain of the Escherichia coli Autotransporter EspP.
Authors: Khan, S. / Mian, H.S. / Sandercock, L.E. / Chirgadze, N.Y. / Pai, E.F.
History
DepositionJul 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine protease espP


Theoretical massNumber of molelcules
Total (without water)105,5351
Polymers105,5351
Non-polymers00
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.340, 88.340, 311.533
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Serine protease espP / Secreted autotransporter protein espP / Extracellular serine protease plasmid-encoded espP


Mass: 105535.258 Da / Num. of mol.: 1 / Fragment: passenger domain, UNP residues 56-1023 / Mutation: S263A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Strain: EDL933 / Gene: ECO57PM78, espP, L7020 / Plasmid: pB9-5-S263A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q7BSW5, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.88 Å3/Da / Density % sol: 57.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18 22% PEG 4000, 0.1M HEPES, 0.05 0.15M tri-lithium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 23, 2007
RadiationMonochromator: bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9002 Å / Relative weight: 1
ReflectionResolution: 2.5→85.13 Å / Num. all: 43770 / Num. obs: 43730 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 13.99
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 3.86 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BioCARS-developedGUIdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.909 / SU B: 15.943 / SU ML: 0.178 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(I): 13.99 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23134 2193 5 %RANDOM
Rwork0.18839 ---
obs0.19056 41456 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.213 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å20 Å2
2--1.05 Å20 Å2
3----2.1 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7245 0 0 324 7569
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227381
X-RAY DIFFRACTIONr_bond_other_d0.0010.024789
X-RAY DIFFRACTIONr_angle_refined_deg1.1141.9299999
X-RAY DIFFRACTIONr_angle_other_deg0.787311740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6035942
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.12625.694353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.254151234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2821524
X-RAY DIFFRACTIONr_chiral_restr0.0680.21122
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028404
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021452
X-RAY DIFFRACTIONr_nbd_refined0.1920.21354
X-RAY DIFFRACTIONr_nbd_other0.1910.24995
X-RAY DIFFRACTIONr_nbtor_refined0.1740.23561
X-RAY DIFFRACTIONr_nbtor_other0.0830.24134
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2415
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1910.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.26
X-RAY DIFFRACTIONr_mcbond_it0.4511.56013
X-RAY DIFFRACTIONr_mcbond_other0.0541.51956
X-RAY DIFFRACTIONr_mcangle_it0.52627461
X-RAY DIFFRACTIONr_scbond_it0.87533226
X-RAY DIFFRACTIONr_scangle_it1.3444.52537
LS refinement shellResolution: 2.502→2.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 135 -
Rwork0.254 2958 -
obs--98.19 %
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)
11.61380.0462-0.42911.01080.86732.1245-0.02210.011-0.06950.0106-0.08840.02670.1915-0.25320.1104-0.1017-0.01550.0226-0.1766-0.0143-0.0631-71.6010.54419.873
21.18220.1-0.71150.82550.36482.54450.0384-0.21530.12910.1048-0.0501-0.0179-0.08050.18730.0118-0.15840.0026-0.0323-0.1013-0.0408-0.027-48.26318.01730.162
30.6025-0.0663-0.75181.2744-1.4364.11490.14380.23760.2174-0.2308-0.0592-0.08780.0335-0.1226-0.0846-0.13060.05810.05930.0210.04950.0454-35.38725.081-27.929
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A56 - 313
2X-RAY DIFFRACTION1A569 - 629
3X-RAY DIFFRACTION2A314 - 568
4X-RAY DIFFRACTION2A671 - 697
5X-RAY DIFFRACTION3A630 - 670
6X-RAY DIFFRACTION3A698 - 1023

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