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- PDB-7qfy: Fusarium oxysporum M36 protease without the propeptide -

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Basic information

Entry
Database: PDB / ID: 7qfy
TitleFusarium oxysporum M36 protease without the propeptide
ComponentsExtracellular metalloproteinase
KeywordsRECOMBINATION / Keratinase / Protease / Metalloprotein
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
Similarity search - Domain/homology
Extracellular metalloproteinase
Similarity search - Component
Biological speciesFusarium oxysporum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsWilkens, C. / Qiu, J. / Meyer, A.S. / Morth, J.P.
Funding support China, Denmark, 2items
OrganizationGrant numberCountry
Chinese Scholarship Council201806910049 China
Technical University of Denmark (DTU) Denmark
CitationJournal: To Be Published
Title: Fusarium oxysporum M36 protease without the propeptide
Authors: Wilkens, C. / Qiu, J. / Meyer, A.S. / Morth, J.P.
History
DepositionDec 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 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: Extracellular metalloproteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5405
Polymers41,9701
Non-polymers5704
Water5,855325
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.371, 57.371, 105.895
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

#1: Protein Extracellular metalloproteinase / Fungalysin


Mass: 41970.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium oxysporum (fungus) / Gene: krtC / Production host: Komagataella pastoris (fungus)
References: UniProt: M1UZ70, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#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.: 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
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.08 Å3/Da / Density % sol: 40.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 25% Polyethylene glycol 3,350

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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: 1.618→50.444 Å / Num. obs: 42678 / % possible obs: 97.9 % / Redundancy: 13.6 % / Biso Wilson estimate: 10.95 Å2 / CC1/2: 1 / Net I/σ(I): 14.2
Reflection shellResolution: 1.618→1.646 Å / Num. unique obs: 2196 / CC1/2: 0.7

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Processing

Software
NameVersionClassification
MxCuBE3data collection
autoPROCdata processing
Cootmodel building
PHENIX1.19.2refinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4k90

4k90


Resolution: 1.62→40.57 Å / SU ML: 0.1374 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.7437
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1731 2041 4.78 %
Rwork0.1482 40617 -
obs0.1494 42658 97.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.96 Å2
Refinement stepCycle: LAST / Resolution: 1.62→40.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2950 0 31 325 3306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00823088
X-RAY DIFFRACTIONf_angle_d0.92094212
X-RAY DIFFRACTIONf_chiral_restr0.0526449
X-RAY DIFFRACTIONf_plane_restr0.0099558
X-RAY DIFFRACTIONf_dihedral_angle_d12.63161094
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.660.23921390.20682754X-RAY DIFFRACTION99.55
1.66-1.70.21751390.1942773X-RAY DIFFRACTION99.76
1.7-1.740.25921300.18952738X-RAY DIFFRACTION99.76
1.74-1.790.2141130.17422793X-RAY DIFFRACTION99.83
1.79-1.850.2321050.15522793X-RAY DIFFRACTION99.9
1.85-1.910.1661370.15072496X-RAY DIFFRACTION96.62
1.92-20.16811350.14332496X-RAY DIFFRACTION99.77
2-2.090.19051560.14052741X-RAY DIFFRACTION99.97
2.09-2.20.15441430.14342775X-RAY DIFFRACTION100
2.2-2.330.19241290.13642451X-RAY DIFFRACTION89.43
2.33-2.510.16591390.13012769X-RAY DIFFRACTION99.97
2.51-2.770.15791500.13862752X-RAY DIFFRACTION100
2.77-3.170.17171340.14252776X-RAY DIFFRACTION100
3.17-3.990.15581450.13612703X-RAY DIFFRACTION97.77
3.99-40.570.14461470.152807X-RAY DIFFRACTION99.9
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)
11.084133396290.0931274339421-0.1924244933070.7612870263840.1110974853820.8819298797470.02807426088270.0995762335054-0.0558518967611-0.031692386925-0.00493120123019-0.03202894485870.07218919330490.0616614518107-0.01105451819880.06457134551770.0197951801178-0.004299344867080.0530907579048-0.00704315679880.046599034985515.881244328929.384613780532.9633505381
21.089612847750.2115131551730.1590307366740.15943604935-0.03364289500020.2408249390580.0530571836674-0.1885579840.1863711863230.0398592780151-0.0555341454130.0761769380309-0.00169294006693-0.0933185345014-0.02773012160550.0705781929647-0.008443902035380.006201938392980.101647929613-0.0213406662250.09608942867423.2710297505839.523749314343.94058376
31.1298976405-0.150258519726-0.3749412954210.822556514544-0.2131854467561.085648090450.0587564284585-0.3037876973680.1539908495560.0514853809933-0.04792803153650.06150301164410.0333217926107-0.155745653250.06377652765330.0783305296147-0.03106879287520.01124298738830.224778451773-0.03650933145180.155299045254-12.569408114635.743959868647.8237212287
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 110 )1 - 1101 - 110
22chain 'A' and (resid 111 through 296 )111 - 296111 - 296
33chain 'A' and (resid 297 through 386 )297 - 386297 - 386

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