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- PDB-2qom: The crystal structure of the E.coli EspP autotransporter Beta-domain. -

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Basic information

Entry
Database: PDB / ID: 2qom
TitleThe crystal structure of the E.coli EspP autotransporter Beta-domain.
ComponentsSerine protease espP
KeywordsHYDROLASE / outer membrane protein / beta-barrel / beta-domain / autotransporter / Protease / Secreted / Serine protease / Transmembrane / Virulence / Zymogen
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 / MAD folllowed by Molecular Replacement / Resolution: 2.66 Å
AuthorsBarnard, T.J. / Dautin, N. / Lukacik, P. / Bernstein, H.D. / Buchanan, S.K.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2007
Title: Autotransporter structure reveals intra-barrel cleavage followed by conformational changes.
Authors: Barnard, T.J. / Dautin, N. / Lukacik, P. / Bernstein, H.D. / Buchanan, S.K.
History
DepositionJul 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine protease espP
B: Serine protease espP


Theoretical massNumber of molelcules
Total (without water)62,6732
Polymers62,6732
Non-polymers00
Water1086
1
A: Serine protease espP


Theoretical massNumber of molelcules
Total (without water)31,3371
Polymers31,3371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Serine protease espP


Theoretical massNumber of molelcules
Total (without water)31,3371
Polymers31,3371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)84.951, 53.298, 102.418
Angle α, β, γ (deg.)90.00, 103.57, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
151A
161B
171A
181B
191A
201B
211A
221B
231A
241B
251A
261B
271A
281B
291A
301B
311A
321B
331A
341B
351A
361B
371A
381B
391A
401B
411A
421B
431A
441B
451A
461B
471A
481B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNGLUGLU2AA1024 - 10381 - 15
21ASNASNGLUGLU2BB1024 - 10381 - 15
32ALAALASERSER2AA1039 - 105116 - 28
42ALAALASERSER2BB1039 - 105116 - 28
53ALAALAPHEPHE5AA1052 - 105629 - 33
63ALAALAPHEPHE5BB1052 - 105629 - 33
74SERSERVALVAL2AA1057 - 106734 - 44
84SERSERVALVAL2BB1057 - 106734 - 44
95ASPASPPHEPHE5AA1068 - 107945 - 56
105ASPASPPHEPHE5BB1068 - 107945 - 56
116THRTHRALAALA2AA1080 - 109157 - 68
126THRTHRALAALA2BB1080 - 109157 - 68
137SERSERSERSER5AA1092 - 109769 - 74
147SERSERSERSER5BB1092 - 109769 - 74
158GLYGLYALAALA2AA1098 - 111175 - 88
168GLYGLYALAALA2BB1098 - 111175 - 88
179METMETALAALA5AA1112 - 111789 - 94
189METMETALAALA5BB1112 - 111789 - 94
1910TYRTYRTYRTYR2AA1118 - 113295 - 109
2010TYRTYRTYRTYR2BB1118 - 113295 - 109
2111THRTHRARGARG5AA1133 - 1142110 - 119
2211THRTHRARGARG5BB1133 - 1142110 - 119
2312ASPASPTYRTYR2AA1143 - 1159120 - 136
2412ASPASPTYRTYR2BB1143 - 1159120 - 136
2513HISHISTRPTRP5AA1160 - 1166137 - 143
2613HISHISTRPTRP5BB1160 - 1166137 - 143
2714ILEILEVALVAL2AA1167 - 1178144 - 155
2814ILEILEVALVAL2BB1167 - 1178144 - 155
2915SERSERASPASP5AA1179 - 1196156 - 173
3015SERSERASPASP5BB1179 - 1196156 - 173
3116LYSLYSPHEPHE2AA1197 - 1214174 - 191
3216LYSLYSPHEPHE2BB1197 - 1214174 - 191
3317SERSERTRPTRP5AA1215 - 1219192 - 196
3417SERSERTRPTRP5BB1215 - 1219192 - 196
3518LYSLYSALAALA2AA1220 - 1235197 - 212
3618LYSLYSALAALA2BB1220 - 1235197 - 212
3719ASNASNGLYGLY5AA1236 - 1252213 - 229
3819ASNASNGLYGLY5BB1236 - 1252213 - 229
3920GLUGLUARGARG2AA1253 - 1269230 - 246
4020GLUGLUARGARG2BB1253 - 1269230 - 246
4121ASPASPARGARG5AA1270 - 1273247 - 250
4221ASPASPARGARG5BB1270 - 1273247 - 250
4322PHEPHESERSER2AA1274 - 1281251 - 258
4422PHEPHESERSER2BB1274 - 1281251 - 258
4523ALAALAASNASN5AA1282 - 1287259 - 264
4623ALAALAASNASN5BB1282 - 1287259 - 264
4724VALVALPHEPHE2AA1288 - 1300265 - 277
4824VALVALPHEPHE2BB1288 - 1300265 - 277

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Components

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


Mass: 31336.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: espP / Plasmid: pTrc99A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q7BSW5, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 65.8 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 0.34M Cymal-1, 1% octylglucoside, 33% PEG 1000, 0.2M NaCl, 0.1M Na cacodylate pH 6.4, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-ID10.97180, 0.97925, 0.97947
SYNCHROTRONAPS 22-BM20.97121
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDJul 1, 2006
MAR CCD 225 mm2CCDAug 22, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 220 (ROSENBAUM-ROCK DOUBLE-CRYSTAL MONOCHROMATOR)MADMx-ray1
2Si 111 (Rosenbaum-Rock double-crystal monochromator)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97181
20.979251
30.979471
40.971211
ReflectionResolution: 2.66→50 Å / Num. all: 23299 / Num. obs: 23299 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 13
Reflection shellResolution: 2.66→2.76 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 1.92 / % possible all: 79.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD folllowed by Molecular Replacement
Starting model: from MAD

Resolution: 2.66→15 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.915 / SU B: 36.499 / SU ML: 0.335 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.535 / ESU R Free: 0.326 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28424 1243 5.1 %RANDOM
Rwork0.25825 ---
all0.25959 23299 --
obs0.25959 23299 95.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.36 Å2
Baniso -1Baniso -2Baniso -3
1--8.44 Å20 Å21.8 Å2
2--11.84 Å20 Å2
3----2.56 Å2
Refinement stepCycle: LAST / Resolution: 2.66→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4011 0 0 6 4017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0214122
X-RAY DIFFRACTIONr_bond_other_d0.0010.022702
X-RAY DIFFRACTIONr_angle_refined_deg1.2861.9135562
X-RAY DIFFRACTIONr_angle_other_deg0.92936489
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6325530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.12823.249197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.28715605
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7221526
X-RAY DIFFRACTIONr_chiral_restr0.1240.2581
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024786
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02960
X-RAY DIFFRACTIONr_nbd_refined0.1790.2682
X-RAY DIFFRACTIONr_nbd_other0.1920.22745
X-RAY DIFFRACTIONr_nbtor_refined0.190.21891
X-RAY DIFFRACTIONr_nbtor_other0.0870.22478
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2124
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2540.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2920.218
X-RAY DIFFRACTIONr_mcbond_it2.32102666
X-RAY DIFFRACTIONr_mcbond_other0.798101130
X-RAY DIFFRACTIONr_mcangle_it3.441114086
X-RAY DIFFRACTIONr_scbond_it3.546121697
X-RAY DIFFRACTIONr_scangle_it4.321131473
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1038tight positional0.040.05
1617medium positional0.350.5
503loose positional0.645
1038tight thermal0.130.5
1617medium thermal0.862
503loose thermal3.5210
LS refinement shellResolution: 2.66→2.731 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 62 -
Rwork0.373 1222 -
obs--70.09 %
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)
16.0642-0.5251-1.54331.25070.62922.38530.0372-0.62580.102-0.0197-0.16890.1099-0.1916-0.30310.1317-0.05550.0671-0.0053-0.22810.0085-0.081215.48537.023617.2828
25.039-0.7921-0.57362.30280.52671.8188-0.0911-1.15330.04890.02460.1576-0.384-0.24620.2504-0.0665-0.1389-0.054-0.03180.401-0.0913-0.19350.98254.005528.5539
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1024 - 12781 - 255
2X-RAY DIFFRACTION2BB1024 - 12781 - 255

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