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- PDB-6ait: Crystal structure of E. coli BepA -

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Basic information

Entry
Database: PDB / ID: 6ait
TitleCrystal structure of E. coli BepA
ComponentsBeta-barrel assembly-enhancing protease
KeywordsHYDROLASE / METAL BINDING PROTEIN
Function / homology
Function and homology information


Gram-negative-bacterium-type cell outer membrane assembly / Hydrolases; Acting on peptide bonds (peptidases) / protein disulfide isomerase activity / chaperone-mediated protein folding / proteolysis involved in protein catabolic process / metalloendopeptidase activity / outer membrane-bounded periplasmic space / zinc ion binding / membrane / metal ion binding
Similarity search - Function
Beta-barrel assembly-enhancing protease / Peptidase M48 / Peptidase family M48 / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Beta-barrel assembly-enhancing protease
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.598 Å
AuthorsUmar, M.S.M. / Tanaka, Y. / Kamikubo, H. / Tsukazaki, T.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP26119007 Japan
Japan Society for the Promotion of ScienceJP26119007 Japan
Japan Society for the Promotion of ScienceJP18H02405 Japan
Japan Society for the Promotion of ScienceJP17H05669 Japan
CitationJournal: J. Mol. Biol. / Year: 2019
Title: Structural Basis for the Function of the beta-Barrel Assembly-Enhancing Protease BepA.
Authors: Shahrizal, M. / Daimon, Y. / Tanaka, Y. / Hayashi, Y. / Nakayama, S. / Iwaki, S. / Narita, S.I. / Kamikubo, H. / Akiyama, Y. / Tsukazaki, T.
History
DepositionAug 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2May 22, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-barrel assembly-enhancing protease
B: Beta-barrel assembly-enhancing protease
C: Beta-barrel assembly-enhancing protease
D: Beta-barrel assembly-enhancing protease
E: Beta-barrel assembly-enhancing protease
F: Beta-barrel assembly-enhancing protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)294,45218
Polymers293,3276
Non-polymers1,12512
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint7 kcal/mol
Surface area108540 Å2
Unit cell
Length a, b, c (Å)85.844, 104.674, 104.971
Angle α, β, γ (deg.)113.610, 105.840, 104.030
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Beta-barrel assembly-enhancing protease


Mass: 48887.816 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: bepA, yfgC, b2494, JW2479 / Plasmid: pYD296 / Production host: Escherichia coli (E. coli) / Strain (production host): KRX
References: UniProt: P66948, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Sequence details1st G44 is derived from the plasmid vector, which is the rest of a protease recognition site.

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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: 2.6 Å3/Da / Density % sol: 52.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.598→48.595 Å / Num. obs: 89522 / % possible obs: 98.24 % / Redundancy: 3.7 % / Biso Wilson estimate: 62.48 Å2 / Rmerge(I) obs: 0.1039 / Rpim(I) all: 0.06328 / Rrim(I) all: 0.1219 / Net I/σ(I): 8.88
Reflection shellResolution: 2.598→2.691 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.218 / Num. unique obs: 8738 / Rpim(I) all: 0.7477 / Rrim(I) all: 1.434 / % possible all: 94.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C37, 5XI8

3c37

5xi8


Resolution: 2.598→48.595 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.91
RfactorNum. reflection% reflection
Rfree0.2633 2016 2.25 %
Rwork0.2063 --
obs0.2076 89490 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 209.94 Å2 / Biso mean: 81.268 Å2 / Biso min: 32.75 Å2
Refinement stepCycle: final / Resolution: 2.598→48.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19568 0 54 110 19732
Biso mean--86.44 56.41 -
Num. residues----2483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00419927
X-RAY DIFFRACTIONf_angle_d0.61326934
X-RAY DIFFRACTIONf_chiral_restr0.0392918
X-RAY DIFFRACTIONf_plane_restr0.0033629
X-RAY DIFFRACTIONf_dihedral_angle_d9.48212190
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5978-2.66280.3881370.355994613194
2.6628-2.73480.34471450.32146211635698
2.7348-2.81520.34081410.28986234637598
2.8152-2.90610.30751520.27436224637698
2.9061-3.00990.35061310.27266282641398
3.0099-3.13040.34971440.27916296644098
3.1304-3.27290.32191400.25376244638498
3.2729-3.44540.31291550.24076268642398
3.4454-3.66120.28521350.22296249638499
3.6612-3.94370.2821580.20146268642699
3.9437-4.34040.23641450.17646303644899
4.3404-4.96790.23061530.17486299645299
4.9679-6.2570.25971390.19646322646199
6.257-48.60360.17621410.14316280642199
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)
13.85420.07170.26173.69580.46383.80220.06890.8022-0.1968-0.4146-0.07-0.117-0.21530.2228-0.0120.31740.03810.00420.6791-0.09630.3737-108.2243-30.23742.3372
24.2284-0.41070.55144.0938-1.71716.22260.03311.23760.207-0.4656-0.2881-0.2469-0.47560.21550.19010.47010.0682-0.01030.83330.01670.5283-113.7057-22.3747-4.2625
39.06194.02811.93268.82480.0472.8119-0.18090.74180.55390.05320.0488-0.1529-0.27810.19350.15020.4640.04150.02260.7924-0.00590.4518-113.4465-19.7991-0.6547
48.39493.25010.56848.7611-0.10871.4035-0.10080.110.52790.14530.0050.7475-0.0204-0.48120.11310.35350.07350.05580.7171-0.10160.559-125.7951-22.22877.8421
52.3572-1.5095-0.09983.2426-0.13612.5622-0.3132-0.0729-0.63360.02140.20810.42710.4822-0.38370.13060.4302-0.15540.15860.5872-0.0680.5371-110.8416-45.499121.016
62.37111.4466-1.56192.6587-0.66192.4567-0.19310.0819-0.35770.02670.0703-0.01660.22330.10880.10430.4138-0.02560.1250.473-0.10750.5503-88.0785-44.65095.3184
74.7015-4.57792.09264.5853-2.58368.1110.25280.72760.1314-1.053-0.2681-0.5018-0.1368-0.23490.04860.4061-0.10860.10180.6189-0.10770.5874-83.5083-34.6311-7.8542
84.14811.07851.94897.52071.84988.02960.02110.2852-0.23920.0607-0.19540.5707-0.0846-0.38750.15250.3588-0.04170.07310.2960.00860.5348-154.1009-4.622316.151
96.75161.90631.08466.43361.08015.8231-0.11690.30730.586-0.5114-0.1911-0.0546-0.547-0.1850.35920.49240.0287-0.03320.28590.04210.4729-149.97643.810313.614
103.98842.84172.75356.06153.61788.6748-0.45390.64620.3253-0.91520.1459-0.1107-0.1078-0.05460.2570.8484-0.00920.03950.55520.06680.5881-150.81387.36428.1868
115.20292.77720.26186.09033.57498.1533-0.16860.1944-0.0907-0.85540.4813-0.9847-1.13881.1824-0.20980.7733-0.17120.05610.55410.03840.7372-137.821811.92211.6718
124.85422.6921.31688.91793.75266.72990.2425-0.47470.94030.195-0.0429-0.3324-2.07790.4911-0.10610.811-0.11870.12270.4251-0.09731.0522-142.379919.546221.923
135.7643-0.15791.59622.74510.20176.66180.2222-0.1691-0.07990.7401-0.0992-1.5128-0.13150.8976-0.06710.5491-0.0646-0.2150.60470.01011.1026-130.2143-7.829627.2106
145.35911.30233.04655.3541.01465.77670.0785-0.4007-0.33251.0333-0.2422-0.6030.30.01610.14890.46140.0097-0.05140.39040.06950.4606-148.9735-22.446828.2636
157.50234.3171-2.9852.7456-2.20756.2848-0.5420.5266-0.13-0.24050.29180.35380.1214-0.91750.13670.40820.0060.0550.6017-0.17380.5526-166.2083-24.744910.1424
167.41210.61021.42774.4225-0.19426.29230.08740.5245-0.42330.0150.05270.18490.54250.2367-0.11640.31820.0542-0.070.5049-0.03150.4513-88.3914-39.158854.9488
176.53820.35452.4273.4927-0.64546.9650.35840.149-0.40740.153-0.1563-0.1770.33760.5897-0.22340.43710.0724-0.06740.5964-0.06770.5865-76.8129-40.609763.3422
183.6745-0.53141.36712.6002-1.28022.7082-0.89331.24911.2275-0.07670.0274-0.1752-1.3491.28680.64570.8186-0.3922-0.22510.8880.38960.9234-85.7074-17.855643.2283
195.96212.21510.5353.3351-0.77262.9155-0.07280.3495-0.0757-0.1629-0.14480.02190.13310.09750.21040.33820.0490.05940.4923-0.01160.3304-109.472-36.773943.0366
202.5790.13930.67066.3082.3973.2626-0.1352-0.3172-0.42510.6208-0.1310.35060.7303-0.2330.30310.7139-0.03940.14320.46730.03040.5839-133.1668-74.057347.821
217.7591.68182.41663.99591.47915.9864-0.2305-0.4292-0.93410.5085-0.30740.44041.5591-0.14650.34931.19530.09050.29170.4984-0.00171.0321-128.6187-89.081343.3361
222.44220.8858-1.39895.9958-0.61713.2788-0.18850.5363-0.436-1.0601-0.16690.46290.2751-0.20250.39121.05710.014-0.10720.7348-0.23870.6131-139.1902-69.37624.1141
233.55110.47282.47022.69011.78037.40410.1949-0.07230.0505-0.385-0.19050.36290.0554-0.32980.06040.33650.042-0.0220.32660.01140.4797-138.6407-46.392542.1441
244.4545-1.87660.35636.01920.12674.1817-0.2412-0.2052-0.0010.54210.1682-0.43920.43210.99110.08450.58990.09020.03630.7548-0.00920.4319-130.2143-34.558687.8691
252.71261.63040.33158.89242.41344.906-0.1553-0.8424-0.32731.46430.15420.10450.72020.1334-0.04391.0640.19330.09741.02470.09910.5876-137.3318-38.870999.284
261.0655-0.6611-1.06362.20581.06292.73750.02740.01190.18680.0483-0.01050.3669-0.057-0.3841-0.03590.37680.0103-0.00950.4982-0.07930.6844-140.1018-17.011175.2213
277.53822.8629-2.87057.1007-2.67416.6081-0.0317-0.2331-0.25370.1668-0.1153-0.37340.10120.64180.20970.37810.0160.06320.5038-0.15520.4664-116.3089-32.606961.4564
283.7622-3.0224-0.18654.0074-0.84124.08630.47710.06230.3857-2.0765-0.0751-0.244-0.88010.5728-0.36241.1878-0.09010.14580.5004-0.00350.4325-116.424818.205459.7654
293.1791.3502-1.69830.5842-0.53233.86920.44960.91351.0402-1.2091-0.8367-0.1099-0.44630.0609-1.40212.65660.02430.55490.73640.11320.5099-118.029726.409652.0884
303.4917-1.9362-2.97052.0592-0.51356.37760.30880.5758-0.1386-2.0803-0.1903-0.0535-0.4010.0257-0.25072.07810.15350.0860.7727-0.03710.7538-120.335820.86547.6414
312.13-1.4276-1.42964.6666-1.28847.3909-0.16451.46570.7292-1.93230.0975-0.1174-0.8407-0.9929-0.11231.90530.0648-0.09711.10430.10670.8309-119.585420.17938.2391
323.0004-1.2233-0.74276.49510.59112.85750.10530.157-0.2221-1.92150.00650.0159-0.23860.368-0.03440.9411-0.0290.09620.5087-0.13950.6276-111.2707-3.882354.4778
333.1472-1.3157-2.49076.33724.25396.0422-0.1465-0.31710.01840.42880.6952-1.11580.51641.1495-0.47420.39560.1372-0.03110.711-0.11770.6023-105.14641.06274.8027
345.5114-2.4486-0.01984.5679-0.56575.0211-0.1327-0.11490.02790.19570.21060.15670.15450.1374-0.03940.3285-0.08590.09020.4188-0.09330.4442-118.451514.61186.5762
353.3514-3.5213.55725.8139-3.38343.7415-0.22510.1220.65980.10910.0975-0.4959-0.99040.20870.32310.4565-0.04490.12820.5126-0.09620.6872-118.19227.324884.8835
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 45 through 126 )A45 - 126
2X-RAY DIFFRACTION2chain 'A' and (resid 127 through 160 )A127 - 160
3X-RAY DIFFRACTION3chain 'A' and (resid 161 through 214 )A161 - 214
4X-RAY DIFFRACTION4chain 'A' and (resid 215 through 271 )A215 - 271
5X-RAY DIFFRACTION5chain 'A' and (resid 272 through 375 )A272 - 375
6X-RAY DIFFRACTION6chain 'A' and (resid 376 through 461 )A376 - 461
7X-RAY DIFFRACTION7chain 'A' and (resid 462 through 482 )A462 - 482
8X-RAY DIFFRACTION8chain 'B' and (resid 44 through 86 )B44 - 86
9X-RAY DIFFRACTION9chain 'B' and (resid 87 through 160 )B87 - 160
10X-RAY DIFFRACTION10chain 'B' and (resid 161 through 214 )B161 - 214
11X-RAY DIFFRACTION11chain 'B' and (resid 215 through 249 )B215 - 249
12X-RAY DIFFRACTION12chain 'B' and (resid 250 through 271 )B250 - 271
13X-RAY DIFFRACTION13chain 'B' and (resid 272 through 338 )B272 - 338
14X-RAY DIFFRACTION14chain 'B' and (resid 339 through 439 )B339 - 439
15X-RAY DIFFRACTION15chain 'B' and (resid 440 through 482 )B440 - 482
16X-RAY DIFFRACTION16chain 'C' and (resid 44 through 126 )C44 - 126
17X-RAY DIFFRACTION17chain 'C' and (resid 127 through 271 )C127 - 271
18X-RAY DIFFRACTION18chain 'C' and (resid 272 through 375 )C272 - 375
19X-RAY DIFFRACTION19chain 'C' and (resid 376 through 482 )C376 - 482
20X-RAY DIFFRACTION20chain 'D' and (resid 45 through 233 )D45 - 233
21X-RAY DIFFRACTION21chain 'D' and (resid 234 through 262 )D234 - 262
22X-RAY DIFFRACTION22chain 'D' and (resid 263 through 338 )D263 - 338
23X-RAY DIFFRACTION23chain 'D' and (resid 339 through 481 )D339 - 481
24X-RAY DIFFRACTION24chain 'E' and (resid 46 through 160 )E46 - 160
25X-RAY DIFFRACTION25chain 'E' and (resid 161 through 271 )E161 - 271
26X-RAY DIFFRACTION26chain 'E' and (resid 272 through 439 )E272 - 439
27X-RAY DIFFRACTION27chain 'E' and (resid 440 through 481 )E440 - 481
28X-RAY DIFFRACTION28chain 'F' and (resid 45 through 126 )F45 - 126
29X-RAY DIFFRACTION29chain 'F' and (resid 127 through 160 )F127 - 160
30X-RAY DIFFRACTION30chain 'F' and (resid 161 through 232 )F161 - 232
31X-RAY DIFFRACTION31chain 'F' and (resid 233 through 263 )F233 - 263
32X-RAY DIFFRACTION32chain 'F' and (resid 264 through 338 )F264 - 338
33X-RAY DIFFRACTION33chain 'F' and (resid 339 through 409 )F339 - 409
34X-RAY DIFFRACTION34chain 'F' and (resid 410 through 461 )F410 - 461
35X-RAY DIFFRACTION35chain 'F' and (resid 462 through 481 )F462 - 481

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