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- PDB-4er4: HIGH-RESOLUTION X-RAY ANALYSES OF RENIN INHIBITOR-ASPARTIC PROTEI... -

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Basic information

Entry
Database: PDB / ID: 4er4
TitleHIGH-RESOLUTION X-RAY ANALYSES OF RENIN INHIBITOR-ASPARTIC PROTEINASE COMPLEXES
Components
  • ENDOTHIAPEPSIN
  • H-142
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / ACID PROTEINASE / 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
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsFoundling, S.I. / Watson, F.E. / Szelke, M. / Blundell, T.L.
Citation
Journal: Nature / Year: 1987
Title: High resolution X-ray analyses of renin inhibitor-aspartic proteinase complexes.
Authors: Foundling, S.I. / Cooper, J. / Watson, F.E. / Cleasby, A. / Pearl, L.H. / Sibanda, B.L. / Hemmings, A. / Wood, S.P. / Blundell, T.L. / Valler, M.J. / Norey, C.G. / Kay, J. / Boger, J. / ...Authors: Foundling, S.I. / Cooper, J. / Watson, F.E. / Cleasby, A. / Pearl, L.H. / Sibanda, B.L. / Hemmings, A. / Wood, S.P. / Blundell, T.L. / Valler, M.J. / Norey, C.G. / Kay, J. / Boger, J. / Dunn, B.M. / Leckieparallel, B.J. / Jone, D.M. / Atrash, B. / Hallett, A. / Szelke, M.
#1: Journal: FEBS Lett. / Year: 1984
Title: The Active Site of Aspartic Proteinases
Authors: Pearl, L. / Blundell, T.
#2: Journal: Proc.FEBS Meet. / Year: 1979
Title: Active Site of Acid Proteinases
Authors: Blundell, T.L. / Jones, H.B. / Khan, G. / Taylor, G. / Sewell, T.S. / Pearl, L.H. / Wood, S.P.
#3: Journal: Proc.FEBS Meet. / Year: 1979
Title: The Three-Dimensional Structure of Acid Proteinases
Authors: Blundell, T.L. / Jenkins, J.A. / Khan, G. / Roychowdhury, P. / Sewell, T. / Tickle, I.J. / Wood, E.A.
#4: Journal: Biochim.Biophys.Acta / Year: 1979
Title: Four-Fold Structural Repeat in the Acid Proteases
Authors: Blundell, T.L. / Sewell, B.T. / Mclachlan, A.D.
#5: Journal: Nature / Year: 1978
Title: Structural Evidence for Gene Duplication in the Evolution of Acid Proteases
Authors: Tang, J. / James, M.N.G. / Hsu, I.N. / Jenkins, J.A. / Blundell, T.L.
#6: Journal: Proc.Natl.Acad.Sci.USA / Year: 1977
Title: Homology Among Acid Proteases. Comparison of Crystal Structures at 3 Angstroms Resolution of Acid Proteases from Rhizopus Chinensis and Endothia Parasitica
Authors: Subramanian, E. / Swan, I.D.A. / Liu, M. / Davies, D.R. / Jenkins, J.A. / Tickle, I.J. / Blundell, T.L.
#7: Journal: Adv.Exp.Med.Biol. / Year: 1977
Title: X-Ray Analysis and Circular Dichroism of the Acid Protease from Endothia Parasitica and Chymosin
Authors: Jenkins, J. / Tickle, I. / Sewell, T. / Ungaretti, L. / Wollmer, A. / Blundell, T.
History
DepositionJan 5, 1991Processing site: BNL
Revision 1.0Apr 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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 29, 2012Group: Database references
Revision 1.4Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_validate_polymer_linkage ...pdbx_database_status / pdbx_validate_polymer_linkage / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id
Revision 2.1Oct 30, 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

Downloads & links

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Assembly

Deposited unit
E: ENDOTHIAPEPSIN
I: H-142


Theoretical massNumber of molelcules
Total (without water)35,0282
Polymers35,0282
Non-polymers00
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-9 kcal/mol
Surface area13190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.700, 74.000, 45.500
Angle α, β, γ (deg.)90.00, 109.30, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUES PRO E 23 AND PRO E 133 ARE CIS PROLINES.
2: THE PEPTIDE BOND BETWEEN LEU I 6 AND VAL I 7 HAS BEEN REDUC TO PRODUCE THE SEQUENCE LEU I 6 PSI(CH2-NH) VAL I 7

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Components

#1: Protein ENDOTHIAPEPSIN


Mass: 33813.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryphonectria parasitica (chestnut blight fungus)
References: UniProt: P11838, EC: 3.4.23.6
#2: Protein/peptide H-142


Mass: 1214.501 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE PEPTIDE BOND BETWEEN RESIDUE LEU I 6 AND RESIDUE VAL I 7 HAS BEEN REDUCED TO CH2-NH2. IT IS ...THE PEPTIDE BOND BETWEEN RESIDUE LEU I 6 AND RESIDUE VAL I 7 HAS BEEN REDUCED TO CH2-NH2. IT IS REPRESENTED AS LAV IN THE SEQUENCE.
Has protein modificationY
Sequence detailsTHE COMPLETE SEQUENCE WAS DETERMINED BY V. PEDERSEN AS TRYPTIC FRAGMENTS WHICH WERE ALIGNED IN THE ...THE COMPLETE SEQUENCE WAS DETERMINED BY V. PEDERSEN AS TRYPTIC FRAGMENTS WHICH WERE ALIGNED IN THE ELECTRON DENSITY. HOMOLOGY WITH OTHER ASPARTIC PROTEINASES WAS USED TO RESOLVE ALIGNMENT AMBIGUITIES. THE RESIDUE NUMBERING IS BASED ON THAT OF PORCINE PEPSIN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.46 %
Crystal grow
*PLUS
pH: 6.3 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 Msodium phosphate11dihydrogen, can be replaced with 0.1M sodium acetate
22.7 Mammonium sulfate11
310 %acetone11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.1→20 Å / Rfactor Rwork: 0.194
Details: THE QUANTITY GIVEN IN THE TEMPERATURE FACTOR FIELD OF THE *ATOM* AND *HETATM* RECORDS BELOW IS U**2, WHICH IS THE MEAN-SQUARE AMPLITUDE OF ATOMIC VIBRATION. THE TEMPERATURE FACTOR, B, CAN BE ...Details: THE QUANTITY GIVEN IN THE TEMPERATURE FACTOR FIELD OF THE *ATOM* AND *HETATM* RECORDS BELOW IS U**2, WHICH IS THE MEAN-SQUARE AMPLITUDE OF ATOMIC VIBRATION. THE TEMPERATURE FACTOR, B, CAN BE DERIVED BY THE FOLLOWING RELATION - B = 8 * (PI)**2 * U**2. IT IS AN INDICATION OF POSSIBLE ERRORS IN THE REFINEMENT THAT SOME ARE SLIGHTLY NEGATIVE.
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2467 0 0 325 2792
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.02
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d0.043
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Rfactor obs: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: o_plane_restr / Dev ideal: 0.013

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