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- PDB-3slo: Pre-cleavage Structure of the Autotransporter EspP - N1023D mutant -

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Basic information

Entry
Database: PDB / ID: 3slo
TitlePre-cleavage Structure of the Autotransporter EspP - N1023D 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: 2.52 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 1.4Feb 28, 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: Serine protease espP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9149
Polymers34,4621
Non-polymers2,4528
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.140, 121.664, 122.998
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: 34462.004 Da / Num. of mol.: 1
Fragment: Autotransporter protein espP translocator (UNP residues 999-1300)
Mutation: N1023D
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.: 8 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 3.38 Å3/Da / Density % sol: 63.61 %
Crystal growTemperature: 294 K / pH: 7.5
Details: 18% w/v PEG8000, 20% v/v glycerol, 25 mM sodium acetate, 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: 2.52→50 Å / Num. all: 16621 / Num. obs: 16442 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.076 / Χ2: 1.009 / Net I/σ(I): 11.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.52-2.613.90.5715771.117195.6
2.61-2.7140.48915591.015197.5
2.71-2.8440.36616210.962197.2
2.84-2.994.30.27915621.03197.9
2.99-3.174.50.19116261.015198.6
3.17-3.424.70.12216511.022199.8
3.42-3.7650.08216411.0051100
3.76-4.3150.05516861.007199.9
4.31-5.434.90.0417010.9891100
5.43-504.60.0318180.96199.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.59 Å29.75 Å
Translation2.59 Å29.75 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.2.3phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.52→30.42 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.2625 / WRfactor Rwork: 0.2102 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7895 / SU B: 20.991 / SU ML: 0.212 / SU R Cruickshank DPI: 0.3533 / SU Rfree: 0.2644 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.353 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2578 840 5.1 %RANDOM
Rwork0.2082 ---
obs0.2107 16400 98.67 %-
all-16621 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 118.24 Å2 / Biso mean: 69.9132 Å2 / Biso min: 19.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å2-0 Å2
2--0.39 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.52→30.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2307 0 111 50 2468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0212461
X-RAY DIFFRACTIONr_bond_other_d0.0010.021691
X-RAY DIFFRACTIONr_angle_refined_deg1.821.9473280
X-RAY DIFFRACTIONr_angle_other_deg0.92734090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2275305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26723.661112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.03715356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3371513
X-RAY DIFFRACTIONr_chiral_restr0.1120.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022753
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02535
X-RAY DIFFRACTIONr_mcbond_it0.7441.51493
X-RAY DIFFRACTIONr_mcbond_other0.1431.5642
X-RAY DIFFRACTIONr_mcangle_it1.43622346
X-RAY DIFFRACTIONr_scbond_it2.5263968
X-RAY DIFFRACTIONr_scangle_it4.2564.5934
LS refinement shellResolution: 2.52→2.585 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 74 -
Rwork0.267 1097 -
all-1171 -
obs--95.59 %
Refinement TLS params.Method: refined / Origin x: -8.236 Å / Origin y: 2.825 Å / Origin z: -14.163 Å
111213212223313233
T0.0187 Å2-0.007 Å20.0034 Å2-0.5849 Å20.0722 Å2--0.2122 Å2
L1.2312 °20.2097 °20.2782 °2-1.161 °20.3868 °2--1.5375 °2
S-0.0954 Å °-0.1398 Å °-0.1252 Å °0.0734 Å °0.0463 Å °0.1608 Å °-0.0406 Å °0.1687 Å °0.0491 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A995 - 1023
2X-RAY DIFFRACTION1A1024 - 1300

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