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- PDB-7z6t: Aspergillus clavatus M36 protease without the propeptide -

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Basic information

Entry
Database: PDB / ID: 7z6t
TitleAspergillus clavatus M36 protease without the propeptide
ComponentsExtracellular metalloproteinase mep
KeywordsPEPTIDE BINDING PROTEIN / Keratinase / Protease / Metalloprotein / RECOMBINATION
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / proteolysis / extracellular space / zinc ion binding
Similarity search - Function
Peptidase M36, fungalysin / : / Fungalysin metallopeptidase (M36) / FTP domain / Fungalysin/Thermolysin Propeptide Motif / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Extracellular metalloproteinase mep
Similarity search - Component
Biological speciesAspergillus clavatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsWilkens, C. / Qiu, J. / Meyer, A.S. / Morth, J.P.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Scholarship Council201806910049 China
CitationJournal: To Be Published
Title: Aspergillus clavatus M36 protease without the propeptide
Authors: Wilkens, C. / Qiu, J. / Meyer, A.S. / Morth, J.P.
History
DepositionMar 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 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

Downloads & links

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Assembly

Deposited unit
AAA: Extracellular metalloproteinase mep
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,56624
Polymers42,5731
Non-polymers2,99323
Water8,089449
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.826, 85.037, 55.319
Angle α, β, γ (deg.)90.000, 111.303, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein Extracellular metalloproteinase mep / Elastinolytic metalloproteinase mep / Fungalysin mep


Mass: 42573.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus clavatus (mold)
Strain: ATCC 1007 / CBS 513.65 / DSM 816 / NCTC 3887 / NRRL 1 / QM 1276 / 107
Gene: mep, ACLA_060300 / Production host: Komagataella pastoris (fungus)
References: UniProt: A1C4M2, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]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: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2[DManpa1-6]DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_d2-e1_d6-g1_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]{}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-3)-D-mannose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[o1122h][a1122h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][<C6O5>]{[(1+1)][b-D-Manp]{}}LINUCSPDB-CARE

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Non-polymers , 6 types, 470 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.77 Å3/Da / Density % sol: 55.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 0.2 M lithium sulfate, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.51→45.04 Å / Num. obs: 71273 / % possible obs: 98.72 % / Redundancy: 6.3 % / CC1/2: 0.8 / Net I/σ(I): 12.25
Reflection shellResolution: 1.51→1.564 Å / Num. unique obs: 6523 / CC1/2: 0.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHENIX3refinement
MxCuBEdata collection
XDSdata reduction
XDSdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4k90

4k90


Resolution: 1.51→45.04 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.771 / SU ML: 0.063 / Cross valid method: FREE R-VALUE / ESU R: 0.073 / ESU R Free: 0.071
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.196 3523 4.943 %
Rwork0.1775 67750 -
all0.178 --
obs-71273 97.131 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.884 Å2
Baniso -1Baniso -2Baniso -3
1-1.64 Å20 Å20.747 Å2
2---1.571 Å2-0 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.51→45.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2994 0 186 449 3629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0123393
X-RAY DIFFRACTIONr_angle_refined_deg1.7011.6964587
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.195415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60823.036168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.66915497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6821517
X-RAY DIFFRACTIONr_chiral_restr0.1090.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022589
X-RAY DIFFRACTIONr_nbd_refined0.2120.21658
X-RAY DIFFRACTIONr_nbtor_refined0.3210.22292
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.2378
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2360.280
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2280.232
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0970.21
X-RAY DIFFRACTIONr_mcbond_it1.5771.8051625
X-RAY DIFFRACTIONr_mcangle_it2.3592.7062049
X-RAY DIFFRACTIONr_scbond_it3.0332.3361768
X-RAY DIFFRACTIONr_scangle_it4.1433.3512538
X-RAY DIFFRACTIONr_lrange_it7.39327.7695445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.5450.3231930.2754228X-RAY DIFFRACTION81.1193
1.545-1.5870.2552380.2454789X-RAY DIFFRACTION95.4796
1.587-1.6330.2392530.2154772X-RAY DIFFRACTION98.2597
1.633-1.6830.2422450.2034663X-RAY DIFFRACTION98.8918
1.683-1.7380.2252250.1894576X-RAY DIFFRACTION99.1123
1.738-1.7990.1952240.1844396X-RAY DIFFRACTION99.3976
1.799-1.8670.1672150.1584258X-RAY DIFFRACTION99.3117
1.867-1.9440.1992500.174074X-RAY DIFFRACTION99.6084
1.944-2.030.1992150.1753934X-RAY DIFFRACTION99.4487
2.03-2.1290.1922110.1843738X-RAY DIFFRACTION99.1215
2.129-2.2440.2241960.1963522X-RAY DIFFRACTION97.9452
2.244-2.380.1951470.1833348X-RAY DIFFRACTION98.0915
2.38-2.5440.1611540.173164X-RAY DIFFRACTION98.3111
2.544-2.7480.2091610.172919X-RAY DIFFRACTION97.8399
2.748-3.010.1991510.1742680X-RAY DIFFRACTION97.8907
3.01-3.3650.1991280.1652436X-RAY DIFFRACTION97.8253
3.365-3.8840.1671160.1432166X-RAY DIFFRACTION97.8559
3.884-4.7540.1561010.1311829X-RAY DIFFRACTION98.6203
4.754-6.7130.166690.1851439X-RAY DIFFRACTION98.6911
6.713-45.040.221310.245818X-RAY DIFFRACTION98.3778

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