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- PDB-8b57: Structure of prolyl endoprotease from Aspergillus niger CBS 109712 -

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Basic information

Entry
Database: PDB / ID: 8b57
TitleStructure of prolyl endoprotease from Aspergillus niger CBS 109712
ComponentsProlyl Endoprotease from Aspergillus niger CBS 109712
KeywordsHYDROLASE / Endoprotease / proline-specific / S28 peptidase
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsPijning, T. / Vujicic-Zagar, A. / Van der Laan, J.M. / De Jong, R.M. / Dijkstra, B.W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Protein Sci. / Year: 2024
Title: Structural and time-resolved mechanistic investigations of protein hydrolysis by the acidic proline-specific endoprotease from Aspergillus niger.
Authors: Pijning, T. / Vujicic-Zagar, A. / van der Laan, J.M. / de Jong, R.M. / Ramirez-Palacios, C. / Vente, A. / Edens, L. / Dijkstra, B.W.
History
DepositionSep 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.year / _citation_author.name
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prolyl Endoprotease from Aspergillus niger CBS 109712
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,79713
Polymers54,2541
Non-polymers4,54312
Water1,874104
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint72 kcal/mol
Surface area20150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.030, 162.030, 162.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Prolyl Endoprotease from Aspergillus niger CBS 109712


Mass: 54254.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Patent WO2015177152A1 / Source: (gene. exp.) Aspergillus niger (mold) / Gene: ATCC64974_102810, CAN33_0042530 / Production host: Aspergillus niger (mold) / Strain (production host): CBS 109712

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Sugars , 4 types, 7 molecules

#2: 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.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1721.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-j1_h2-i1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: 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.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
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

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Non-polymers , 5 types, 109 molecules

#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.27 Å3/Da / Density % sol: 62.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 26-29% (w/v) PEG 3350, 0.1 M sodium citrate pH 5.0, 0.1 M ammonium tartrate pH 7.2, 20 mM HAc/NaAc pH 5.0, 50 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9195 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9195 Å / Relative weight: 1
ReflectionResolution: 2.42→66.24 Å / Num. obs: 27027 / % possible obs: 100 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 14.5
Reflection shellResolution: 2.42→2.55 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 3897 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
iMOSFLMdata reduction
SCALAdata scaling
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: composite model

Resolution: 2.42→66.24 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / SU B: 13.7 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.292 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20892 1335 4.9 %RANDOM
Rwork0.16956 ---
obs0.17151 25707 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.924 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.42→66.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3845 0 301 104 4250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0184294
X-RAY DIFFRACTIONr_bond_other_d0.0010.0193631
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.895858
X-RAY DIFFRACTIONr_angle_other_deg1.12.6788409
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9165484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02724.076211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34215541
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1251510
X-RAY DIFFRACTIONr_chiral_restr0.0810.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024771
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021003
X-RAY DIFFRACTIONr_mcbond_it1.4742.1581939
X-RAY DIFFRACTIONr_mcbond_other1.4742.1581938
X-RAY DIFFRACTIONr_mcangle_it2.263.2342422
X-RAY DIFFRACTIONr_mcangle_other2.263.2342423
X-RAY DIFFRACTIONr_scbond_it3.3052.8852355
X-RAY DIFFRACTIONr_scbond_other3.3052.8872356
X-RAY DIFFRACTIONr_scangle_other4.7264.1493437
X-RAY DIFFRACTIONr_long_range_B_refined5.76128.1124974
X-RAY DIFFRACTIONr_long_range_B_other5.75328.0764963
LS refinement shellResolution: 2.42→2.483 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 94 -
Rwork0.239 1856 -
obs--99.69 %
Refinement TLS params.Method: refined / Origin x: 28.257 Å / Origin y: 60.631 Å / Origin z: -6.031 Å
111213212223313233
T0.0933 Å20.0512 Å2-0.0709 Å2-0.0441 Å2-0.0171 Å2--0.2036 Å2
L2.0526 °20.5199 °2-0.8665 °2-0.9749 °2-0.1486 °2--1.0897 °2
S0.0148 Å °-0.039 Å °0.1482 Å °-0.1219 Å °0.008 Å °0.2681 Å °0.0729 Å °0.0461 Å °-0.0229 Å °

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