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- PDB-3emy: Crystal structure of Trichoderma reesei aspartic proteinase compl... -

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Basic information

Entry
Database: PDB / ID: 3emy
TitleCrystal structure of Trichoderma reesei aspartic proteinase complexed with pepstatin A
Components
  • Pepstatin
  • Trichoderma reesei Aspartic protease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Trichoderma reesei / aspartic proteinase / Aspartyl protease / Protease / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Aspergillopepsin-like catalytic 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 ...Aspergillopepsin-like catalytic 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 / Aspartic protease pro-precursor
Similarity search - Component
Biological speciesHypocrea jecorina (fungus)
Streptomyces argenteolus subsp. toyonakensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsNascimento, A.S. / Krauchenco, S. / Golubev, A.M. / Gustchina, A. / Wlodawer, A. / Polikarpov, I.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Statistical coupling analysis of aspartic proteinases based on crystal structures of the Trichoderma reesei enzyme and its complex with pepstatin A.
Authors: Nascimento, A.S. / Krauchenco, S. / Golubev, A.M. / Gustchina, A. / Wlodawer, A. / Polikarpov, I.
History
DepositionSep 25, 2008Deposition site: RCSB / Processing site: RCSB
SupersessionOct 7, 2008ID: 3C9Y
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Feb 27, 2013Group: Other
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trichoderma reesei Aspartic protease
B: Pepstatin


Theoretical massNumber of molelcules
Total (without water)35,0852
Polymers35,0852
Non-polymers00
Water11,133618
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-10 kcal/mol
Surface area13530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.276, 74.276, 160.027
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Trichoderma reesei Aspartic protease


Mass: 34399.152 Da / Num. of mol.: 1 / Fragment: UNP residues 79-407 / Source method: isolated from a natural source / Source: (natural) Hypocrea jecorina (fungus) / References: UniProt: Q2WBH2
#2: Protein/peptide Pepstatin / /


Type: Oligopeptide / Class: Enzyme inhibitor / Mass: 685.891 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in Streptomyces
Source: (synth.) Streptomyces argenteolus subsp. toyonakensis (bacteria)
References: Pepstatin
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 618 / Source method: isolated from a natural source / Formula: H2O

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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: 3.15 Å3/Da / Density % sol: 60.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG3350, 50MM potassium phosphate buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.5 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2006
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 1.85→19.468 Å / Num. obs: 37688 / % possible obs: 96.3 % / Observed criterion σ(F): 1.38 / Observed criterion σ(I): 1.38
Reflection shellResolution: 1.85→1.89 Å / % possible all: 95

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
PHENIX(phenix.refine)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→19.468 Å / SU ML: 0.21 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1834 1884 5 %RANDOM
Rwork0.1413 ---
obs0.1434 37688 96.51 %-
all-39051 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.835 Å2 / ksol: 0.363 e/Å3
Refinement stepCycle: LAST / Resolution: 1.85→19.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2477 0 0 618 3095
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.024
X-RAY DIFFRACTIONf_angle_deg2.041
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90020.22711380.18762532X-RAY DIFFRACTION91
1.9002-1.95610.23461420.16682664X-RAY DIFFRACTION95
1.9561-2.01910.20221230.15182682X-RAY DIFFRACTION95
2.0191-2.09120.19681280.13692701X-RAY DIFFRACTION96
2.0912-2.17480.19491530.13292704X-RAY DIFFRACTION96
2.1748-2.27370.17121320.142719X-RAY DIFFRACTION97
2.2737-2.39330.19741640.14482756X-RAY DIFFRACTION97
2.3933-2.5430.19521450.13462750X-RAY DIFFRACTION98
2.543-2.73890.17061470.12992788X-RAY DIFFRACTION98
2.7389-3.01360.18571620.13032800X-RAY DIFFRACTION99
3.0136-3.44750.15671700.12952824X-RAY DIFFRACTION99
3.4475-4.33560.16541410.11612893X-RAY DIFFRACTION98
4.3356-19.46920.15791390.13822991X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 8.4035 Å / Origin y: 54.3117 Å / Origin z: 7.5643 Å
111213212223313233
T0.0821 Å20.013 Å20.0042 Å2-0.115 Å20.0027 Å2--0.1202 Å2
L0.4762 °20.0676 °20.3309 °2-0.2398 °20.0198 °2--0.6634 °2
S0.0132 Å °0.0609 Å °-0.0301 Å °0.0022 Å °0.001 Å °-0.0603 Å °0.0221 Å °0.0884 Å °-0.0181 Å °
Refinement TLS groupSelection details: all

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