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- PDB-1gkt: Neutron Laue diffraction structure of endothiapepsin complexed wi... -

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Basic information

Entry
Database: PDB / ID: 1gkt
TitleNeutron Laue diffraction structure of endothiapepsin complexed with transition state analogue inhibitor H261
Components
  • ENDOTHIAPEPSIN
  • INHIBITOR, H261Enzyme inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / PROTEASE-INHIBITOR / ASPARTIC PROTEINASE / HYDROLYSIS / HYDROLASE- HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


endothiapepsin / 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
H-261 Oligopeptide / Endothiapepsin
Similarity search - Component
Biological speciesCRYPHONECTRIA PARASITICA (chestnut blight fungus)
synthetic construct (others)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / Resolution: 2.1 Å
AuthorsCoates, L. / Erskine, P.T. / Wood, S.P. / Myles, D.A.A. / Cooper, J.B.
CitationJournal: Biochemistry / Year: 2001
Title: A Neutron Laue Diffraction Study of Endothiapepsin: Implications for the Aspartic Proteinase Mechanism
Authors: Coates, L. / Erskine, P.T. / Wood, S.P. / Myles, D.A.A. / Cooper, J.B.
History
DepositionAug 20, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2001Provider: 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 1.2Nov 30, 2012Group: Other
Revision 1.3Jan 16, 2013Group: Atomic model / Other
Revision 1.4Mar 6, 2013Group: Other
Revision 1.5Mar 22, 2017Group: Atomic model / Data collection
Revision 1.6Feb 14, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_wavelength / _diffrn_source.pdbx_wavelength_list
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_validate_peptide_omega.auth_comp_id_1 / _pdbx_validate_peptide_omega.auth_comp_id_2 / _pdbx_validate_peptide_omega.auth_seq_id_1 / _pdbx_validate_peptide_omega.auth_seq_id_2 / _pdbx_validate_peptide_omega.omega / _struct_conn.pdbx_leaving_atom_flag
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDOTHIAPEPSIN
B: INHIBITOR, H261


Theoretical massNumber of molelcules
Total (without water)34,8992
Polymers34,8992
Non-polymers00
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-5 kcal/mol
Surface area14540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.100, 75.700, 42.900
Angle α, β, γ (deg.)90.00, 97.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ENDOTHIAPEPSIN /


Mass: 33795.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) CRYPHONECTRIA PARASITICA (chestnut blight fungus)
References: UniProt: P11838, endothiapepsin
#2: Protein/peptide INHIBITOR, H261 / Enzyme inhibitor


Type: Peptide-like / Class: Inhibitor / Mass: 1103.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: H-261 Oligopeptide
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity % sol: 39 %
Description: HYDROGEN/DEUTERIUM EXCHANGE BY CAPILLARY VAPOUR DIFFUSION.
Crystal growpH: 4.5 / Details: AS FOR 2ER7, PH 4.5
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.0 mg/mlenzyme11
2100 mMsodium acetate11pH4.5
355 %satammonium sulfate11

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: NUCLEAR REACTOR / Site: ILL / Beamline: LADI / Wavelength: 2.7-3.6
DetectorDetector: IMAGE PLATE / Date: Nov 1, 1999
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
12.71
23.61
ReflectionResolution: 2.1→20 Å / Num. obs: 13548 / % possible obs: 85 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 5.4
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.119 / Mean I/σ(I) obs: 1.7 / % possible all: 72.6
Reflection
*PLUS
Lowest resolution: 100 Å / % possible obs: 84.5 %
Reflection shell
*PLUS
% possible obs: 72.6 %

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Processing

Software
NameClassification
SHELXL-97refinement
LAUEGENdata reduction
SCALAdata scaling
RefinementResolution: 2.1→20 Å / Num. parameters: 20487 / Num. restraintsaints: 97252 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.274 687 5 %RANDOM
obs0.235 -85 %-
all-13548 --
Solvent computationSolvent model: MOEWS & KRETSINGER
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2467 0 0 255 2722
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONs_bond_d0.009
NEUTRON DIFFRACTIONs_angle_d0.014
NEUTRON DIFFRACTIONs_similar_dist
NEUTRON DIFFRACTIONs_from_restr_planes0.023
NEUTRON DIFFRACTIONs_zero_chiral_vol0.023
NEUTRON DIFFRACTIONs_non_zero_chiral_vol0.027
NEUTRON DIFFRACTIONs_anti_bump_dis_restr0.051
NEUTRON DIFFRACTIONs_rigid_bond_adp_cmpnt
NEUTRON DIFFRACTIONs_similar_adp_cmpnt
NEUTRON DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.2346 / Rfactor Rfree: 0.2742 / Rfactor Rwork: 0.235
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.023
X-RAY DIFFRACTIONs_chiral_restr0.027
LS refinement shell
*PLUS
Rfactor obs: 0.331

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