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- PDB-3slj: Pre-cleavage Structure of the Autotransporter EspP - N1023A mutant -

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Basic information

Entry
Database: PDB / ID: 3slj
TitlePre-cleavage Structure of the Autotransporter EspP - N1023A mutant
ComponentsSerine protease espP
KeywordsPROTEIN TRANSPORT / beta barrel / membrane protein / asparagine cyclization / autocleavage
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
Autotransporter beta-domain / 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 / 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 / Pectin lyase fold/virulence factor / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Serine protease EspP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.481 Å
AuthorsBarnard, T.B. / Noinaj, N. / Easley, N.C. / Kuszak, A.J. / Buchanan, S.K.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Molecular basis for the activation of a catalytic asparagine residue in a self-cleaving bacterial autotransporter.
Authors: Barnard, T.J. / Gumbart, J. / Peterson, J.H. / Noinaj, N. / Easley, N.C. / Dautin, N. / Kuszak, A.J. / Tajkhorshid, E. / Bernstein, H.D. / Buchanan, S.K.
History
DepositionJun 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Database references
Revision 1.2Jan 18, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Serine protease espP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,17610
Polymers34,4181
Non-polymers2,7589
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.142, 122.027, 123.641
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Serine protease espP


Mass: 34417.996 Da / Num. of mol.: 1
Fragment: Autotransporter protein espP translocator (UNP residues 999-1300)
Mutation: N1023A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: ECO57PM78, espP, L7020 / Plasmid: pTrc99a / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express / References: UniProt: Q7BSW5
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 3.41 Å3/Da / Density % sol: 63.96 %
Crystal growTemperature: 294 K / pH: 7.5
Details: 20% w/v PEG8000, 20% v/v glycerol, pH 7.5, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 18, 2009 / Details: mirrors
RadiationMonochromator: Si 220 (ROSENBAUM-ROCK DOUBLE-CRYSTAL MONOCHROMATOR)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.48→50 Å / Num. all: 17548 / Num. obs: 17443 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.087 / Χ2: 1.04 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.48-2.574.80.61817281.011100
2.57-2.674.80.49816921.035199.8
2.67-2.794.80.32917221.0131100
2.79-2.944.80.27417001.011199.7
2.94-3.124.80.16717431.026199.5
3.12-3.374.90.11417141.0871100
3.37-3.74.80.07817281.068199.4
3.7-4.244.80.06617561.049199.3
4.24-5.344.70.0517751.003198.7
5.34-504.40.04818851.095198

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 50.9 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å43.41 Å
Translation2.5 Å43.41 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QOM

2qom


Resolution: 2.481→43.426 Å / Occupancy max: 1 / Occupancy min: 0.41 / FOM work R set: 0.8267 / SU ML: 0.35 / σ(F): 1.34 / Phase error: 23.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2374 879 5.06 %RANDOM
Rwork0.1988 ---
obs0.2008 17370 99.01 %-
all-17544 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.558 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso max: 99.98 Å2 / Biso mean: 46.1032 Å2 / Biso min: 18.96 Å2
Baniso -1Baniso -2Baniso -3
1--14.1307 Å20 Å20 Å2
2--0.5637 Å2-0 Å2
3---13.567 Å2
Refinement stepCycle: LAST / Resolution: 2.481→43.426 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2307 0 128 55 2490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072490
X-RAY DIFFRACTIONf_angle_d1.0633316
X-RAY DIFFRACTIONf_chiral_restr0.071334
X-RAY DIFFRACTIONf_plane_restr0.003423
X-RAY DIFFRACTIONf_dihedral_angle_d15.016911
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4807-2.63610.31531530.22542659281298
2.6361-2.83960.23341380.192927322870100
2.8396-3.12530.24191510.182695284699
3.1253-3.57730.23271390.164927212860100
3.5773-4.50630.20691620.1682779294199
4.5063-43.43220.23961360.22662905304198
Refinement TLS params.

S33: 0 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.04160.03460.00820.02730.0064-0.0007-0.0528-0.3485-0.2348-0.00410.02580.12750.45730.35630.5040.05610.00340.3640.04290.5656-1.7128-33.4201-42.2938
21.16760.07970.02870.8407-0.09910.4215-0.0273-0.0567-0.0993-0.12130.03120.02720.02840.13310.2312-0.0067-0.01170.24140.06650.22460.4874-14.9835-33.2321
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resseq 996:1022))A0
2X-RAY DIFFRACTION2chain 'A' and ((resseq 1023:1300))A0

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