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- PDB-7wab: Crystal structure of the prolyl endoprotease, PEP, from Aspergill... -

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Basic information

Entry
Database: PDB / ID: 7wab
TitleCrystal structure of the prolyl endoprotease, PEP, from Aspergillus niger
ComponentsCOMPASS (Complex proteins associated with Set1p) component shg1 family protein
KeywordsHYDROLASE / Protease
Function / homologyPeptidase S28 / Serine carboxypeptidase S28 / serine-type exopeptidase activity / dipeptidyl-peptidase activity / Alpha/Beta hydrolase fold / proteolysis / COMPASS (Complex proteins associated with Set1p) component shg1 family protein
Function and homology information
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMiyazono, K. / Kubota, K. / Takahashi, K. / Tanokura, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Crystal structure and substrate recognition mechanism of the prolyl endoprotease PEP from Aspergillus niger.
Authors: Miyazono, K.I. / Kubota, K. / Takahashi, K. / Tanokura, M.
History
DepositionDec 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COMPASS (Complex proteins associated with Set1p) component shg1 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3845
Polymers54,4441
Non-polymers1,9404
Water9,494527
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.517, 144.517, 56.542
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-1096-

HOH

21A-1168-

HOH

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Components

#1: Protein COMPASS (Complex proteins associated with Set1p) component shg1 family protein / prolyl endoprotease / PEP


Mass: 54444.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Aspergillus niger (mold) / References: UniProt: A0A3F3RXI7
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_d2-e1_e2-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.71 Å3/Da / Density % sol: 54.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 2.5
Details: 0.1M glycine buffer pH 2.5, 2.72M NaCl, 3% isopropanol

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.75→44.53 Å / Num. obs: 107457 / % possible obs: 93.2 % / Redundancy: 7.2 % / Biso Wilson estimate: 25.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.022 / Rrim(I) all: 0.066 / Net I/σ(I): 17.5
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
1.75-1.783.60.422898124910.810.2450.491.875.6
9.09-44.537.30.03432244410.9990.0120.03732.488.2

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Processing

Software
NameVersionClassification
Aimless0.5.17data scaling
PHENIX1.19refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→17.14 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0.04 / Phase error: 20.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1931 5492 5.11 %
Rwork0.1639 101965 -
obs0.1654 107457 93.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.68 Å2 / Biso mean: 31.1361 Å2 / Biso min: 15.07 Å2
Refinement stepCycle: final / Resolution: 1.75→17.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3858 0 128 527 4513
Biso mean--41.33 38.69 -
Num. residues----484
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.770.31161410.2342726286774
1.77-1.790.25361530.22842845299879
1.79-1.810.26111940.21212948314281
1.81-1.830.26491570.21663068322584
1.83-1.860.23431540.20873083323785
1.86-1.880.26611420.22713200334286
1.88-1.910.22822090.23633205341489
1.91-1.940.28661900.23853257344790
1.94-1.970.26442080.20873398360694
1.97-20.21621510.18523597374897
2-2.040.21741560.18193646380298
2.04-2.070.22372290.17453566379599
2.07-2.110.20761860.17683557374398
2.11-2.160.25261640.16843649381399
2.16-2.20.19632130.16413565377899
2.2-2.250.22541850.17563615380098
2.25-2.310.23131740.17563554372898
2.31-2.370.21382020.17853579378198
2.37-2.440.23421690.16963607377698
2.44-2.520.22242220.17763548377098
2.52-2.610.22041820.17673575375798
2.61-2.720.22332290.1793548377797
2.72-2.840.23041790.18163544372397
2.84-2.990.20711530.17213580373397
2.99-3.170.19311710.16763517368896
3.17-3.420.16311930.15263444363795
3.42-3.760.16631920.13633456364895
3.76-4.290.14092160.12183385360194
4.29-5.380.14521970.12913373357093
5.38-17.140.15931810.15683330351191
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)
15.75121.60853.30462.33031.63443.02060.1125-0.5890.40050.1368-0.11210.11960.0603-0.40630.01540.18310.00590.02360.23140.02680.35882.154851.0784-5.8928
23.2081.54250.55941.75820.52981.007-0.04450.12070.5174-0.0590.02980.0505-0.06470.07460.00320.17190.0183-0.03550.16220.03260.28311.875848.0256-9.6322
30.44860.1125-0.5360.4629-0.28050.93370.008-0.1419-0.01230.062-0.0699-0.05810.01370.1130.06390.1518-0.0136-0.04020.19330.01880.16590.967928.2566.7304
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 43 through 102 )A43 - 102
2X-RAY DIFFRACTION2chain 'A' and (resid 103 through 172 )A103 - 172
3X-RAY DIFFRACTION3chain 'A' and (resid 173 through 526 )A173 - 526

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