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- PDB-1wkr: Crystal structure of aspartic proteinase from Irpex lacteus -

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Basic information

Entry
Database: PDB / ID: 1wkr
TitleCrystal structure of aspartic proteinase from Irpex lacteus
Components
  • Polyporopepsin
  • pepstatin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / hydrolase / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


polyporopepsin / aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Pepsin-like domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily ...Pepsin-like domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Pepstatin / Polyporopepsin
Similarity search - Component
Biological speciesIrpex lacteus (fungus)
Streptomyces argenteolus subsp. toyonakensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsFujimoto, Z. / Fujii, Y. / Kaneko, S. / Kobayashi, H. / Mizuno, H.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal Structure of Aspartic Proteinase from Irpex lacteus in Complex with Inhibitor Pepstatin
Authors: Fujimoto, Z. / Fujii, Y. / Kaneko, S. / Kobayashi, H. / Mizuno, H.
History
DepositionJun 2, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Feb 27, 2013Group: Other
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyporopepsin
I: pepstatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4119
Polymers35,7382
Non-polymers6727
Water12,647702
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-83 kcal/mol
Surface area13100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.270, 78.898, 54.072
Angle α, β, γ (deg.)90.00, 96.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Polyporopepsin / Aspartic proteinase


Mass: 35052.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Irpex lacteus (fungus) / References: UniProt: P17576, polyporopepsin
#2: Protein/peptide pepstatin


Type: Oligopeptide / Class: Enzyme inhibitor / Mass: 685.891 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized
Source: (synth.) Streptomyces argenteolus subsp. toyonakensis (bacteria)
References: Pepstatin
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 702 / Source method: isolated from a natural source / Formula: H2O
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: 2.31 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 50% saturated ammonium phosphate, 10mM sodium citrate-sulfate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: May 31, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. all: 77021 / Num. obs: 75525 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 8.6 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 25.4
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 4.9 / Num. unique all: 7488 / % possible all: 98.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4pep

4pep


Resolution: 1.3→26.99 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 827198.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.171 3789 5 %RANDOM
Rwork0.147 ---
obs0.147 75485 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.3823 Å2 / ksol: 0.352801 e/Å3
Displacement parametersBiso mean: 10.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20.42 Å2
2---0.13 Å20 Å2
3---0.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.12 Å0.1 Å
Luzzati d res low-5 Å
Luzzati sigma a0.06 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.3→26.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2520 0 35 702 3257
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.034
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d3.01
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.911.5
X-RAY DIFFRACTIONc_mcangle_it1.212
X-RAY DIFFRACTIONc_scbond_it1.942
X-RAY DIFFRACTIONc_scangle_it2.352.5
LS refinement shellResolution: 1.3→1.38 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.195 639 5.1 %
Rwork0.175 11862 -
obs--98.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4CIS_PEPTIDE.PARAM

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