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- PDB-6sar: E coli BepA/YfgC -

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Basic information

Entry
Database: PDB / ID: 6sar
TitleE coli BepA/YfgC
ComponentsBeta-barrel assembly-enhancing protease
KeywordsCHAPERONE / outer membrane bam complex chaperone protease
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 / MAD / Resolution: 2.18 Å
AuthorsLovering, A.L. / Cadby, I.T.
CitationJournal: J.Bacteriol. / Year: 2020
Title: Structure-Function Characterization of the Conserved Regulatory Mechanism of the Escherichia coli M48 Metalloprotease BepA.
Authors: Bryant, J.A. / Cadby, I.T. / Chong, Z.S. / Boelter, G. / Sevastsyanovich, Y.R. / Morris, F.C. / Cunningham, A.F. / Kritikos, G. / Meek, R.W. / Banzhaf, M. / Chng, S.S. / Lovering, A.L. / Henderson, I.R.
History
DepositionJul 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-barrel assembly-enhancing protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1243
Polymers53,9631
Non-polymers1612
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-7 kcal/mol
Surface area18530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.120, 77.020, 124.600
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 Beta-barrel assembly-enhancing protease


Mass: 53962.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: bepA, yfgC, b2494, JW2479 / Production host: Escherichia coli (E. coli)
References: UniProt: P66948, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.36 Å3/Da / Density % sol: 47.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M Na HEPES, pH 7.0, and 8% w/v PEG 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.28274 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28274 Å / Relative weight: 1
ReflectionResolution: 2.18→77.02 Å / Num. obs: 27140 / % possible obs: 98.9 % / Redundancy: 16.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.028 / Rrim(I) all: 0.119 / Net I/σ(I): 20.8 / Num. measured all: 448076 / Scaling rejects: 467
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.18-2.2460.6161080918000.8170.2670.6752.791.5
9.75-77.0215.10.06156613750.9980.0160.06353.599.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.17data scaling
SHELXphasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.18→77.02 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.955 / SU B: 9.6 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2007 1319 4.9 %RANDOM
Rwork0.1763 ---
obs0.1775 25763 98.84 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 116.01 Å2 / Biso mean: 47.398 Å2 / Biso min: 24.94 Å2
Baniso -1Baniso -2Baniso -3
1--3.52 Å2-0 Å20 Å2
2--2.82 Å2-0 Å2
3---0.7 Å2
Refinement stepCycle: final / Resolution: 2.18→77.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3113 0 6 120 3239
Biso mean--65.52 48.86 -
Num. residues----392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193207
X-RAY DIFFRACTIONr_bond_other_d0.0010.023037
X-RAY DIFFRACTIONr_angle_refined_deg0.9971.9524346
X-RAY DIFFRACTIONr_angle_other_deg0.72136933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4345400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.56724.389180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63415550
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5871531
X-RAY DIFFRACTIONr_chiral_restr0.0590.2467
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023796
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02811
LS refinement shellResolution: 2.18→2.237 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 87 -
Rwork0.254 1710 -
all-1797 -
obs--91.13 %
Refinement TLS params.Method: refined / Origin x: 29.966 Å / Origin y: 48.42 Å / Origin z: 44.623 Å
111213212223313233
T0.1317 Å20.0134 Å20.0157 Å2-0.0046 Å2-0.015 Å2--0.116 Å2
L3.1269 °20.5961 °20.4905 °2-0.8498 °20.2996 °2--1.0287 °2
S-0.0023 Å °-0.0158 Å °-0.1421 Å °0.0586 Å °-0.0033 Å °0.0451 Å °0.0505 Å °0.0179 Å °0.0055 Å °

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