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- PDB-4k90: Extracellular metalloproteinase from Aspergillus -

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Basic information

Entry
Database: PDB / ID: 4k90
TitleExtracellular metalloproteinase from Aspergillus
Components(Extracellular metalloproteinase ...) x 2
KeywordsHYDROLASE / M36 protease
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) / Elastase; domain 1 - #10 / Elastase; domain 1 / FTP domain / Fungalysin/Thermolysin Propeptide Motif / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily ...Peptidase M36, fungalysin / : / Fungalysin metallopeptidase (M36) / Elastase; domain 1 - #10 / Elastase; domain 1 / FTP domain / Fungalysin/Thermolysin Propeptide Motif / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BORIC ACID / MALONIC ACID / Extracellular metalloproteinase mep
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFernandez, D. / Russi, S. / Vendrell, J. / Monod, M. / Pallares, I.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: A functional and structural study of the major metalloprotease secreted by the pathogenic fungus Aspergillus fumigatus.
Authors: Fernandez, D. / Russi, S. / Vendrell, J. / Monod, M. / Pallares, I.
History
DepositionApr 19, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Structure summary
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Extracellular metalloproteinase mep
B: Extracellular metalloproteinase mep
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,92013
Polymers65,6222
Non-polymers1,29811
Water9,368520
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6920 Å2
ΔGint-67 kcal/mol
Surface area21330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.398, 85.398, 176.092
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Extracellular metalloproteinase ... , 2 types, 2 molecules AB

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


Mass: 42157.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: mep, AFUA_8G07080 / Production host: pichia pastoris (fungus)
References: UniProt: P46075, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Protein Extracellular metalloproteinase mep / Elastinolytic metalloproteinase mep / Fungalysin mep


Mass: 23464.953 Da / Num. of mol.: 1 / Fragment: Prodomain, UNP RESIDUES 31-245
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: mep, AFUA_8G07080 / Production host: Pichia pastoris (fungus)
References: UniProt: P46075, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases

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Sugars , 1 types, 1 molecules

#3: 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: isolated from a genetically manipulated source
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)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE

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Non-polymers , 6 types, 530 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#7: Chemical ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: BH3O3
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE EXPERIMENTAL INFO OF UNIPROT P46075 (ELM_ASPFU) SHOWS S -> P, CORRESPONDING TO STRAIN DELTA 18 ...THE EXPERIMENTAL INFO OF UNIPROT P46075 (ELM_ASPFU) SHOWS S -> P, CORRESPONDING TO STRAIN DELTA 18 IN MOL. MICROBIOL. 14:917-928, JATON-OGAY ET AL(1994).

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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: 2.82 Å3/Da / Density % sol: 56.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 20% PEG 1500, malonate/imidazole/borate buffer, pH 4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 19, 2011
RadiationMonochromator: channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 67131 / Num. obs: 67131 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 7.2 % / Biso Wilson estimate: 19.939 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.067 / Net I/σ(I): 22.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 4.3 / Num. unique all: 9812 / Rsym value: 0.188 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→21 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.161 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19797 3395 5.1 %RANDOM
Rwork0.16691 ---
all0.16845 67131 --
obs0.16845 63642 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å2-0.4 Å20 Å2
2---0.79 Å20 Å2
3---1.19 Å2
Refinement stepCycle: LAST / Resolution: 1.8→21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4523 0 79 520 5122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224740
X-RAY DIFFRACTIONr_angle_refined_deg1.2061.9546457
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9535596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79824.808208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6415703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0461518
X-RAY DIFFRACTIONr_chiral_restr0.0860.2718
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023633
X-RAY DIFFRACTIONr_nbd_refined0.1950.22363
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23296
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2397
X-RAY DIFFRACTIONr_metal_ion_refined0.0840.211
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.231
X-RAY DIFFRACTIONr_mcbond_it0.6931.53029
X-RAY DIFFRACTIONr_mcangle_it1.12824769
X-RAY DIFFRACTIONr_scbond_it1.67431978
X-RAY DIFFRACTIONr_scangle_it2.4354.51686
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 258 -
Rwork0.224 4690 -
obs-4690 100 %

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