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- PDB-5pep: X-RAY ANALYSES OF ASPARTIC PROTEASES. II. THREE-DIMENSIONAL STRUC... -

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Basic information

Entry
Database: PDB / ID: 5pep
TitleX-RAY ANALYSES OF ASPARTIC PROTEASES. II. THREE-DIMENSIONAL STRUCTURE OF THE HEXAGONAL CRYSTAL FORM OF PORCINE PEPSIN AT 2.3 ANGSTROMS RESOLUTION
ComponentsPEPSIN
KeywordsHYDROLASE(ACID PROTEINASE)
Function / homology
Function and homology information


Surfactant metabolism / pepsin A / digestion / aspartic-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Pepsin catalytic domain / Aspartic peptidase, N-terminal / A1 Propeptide / 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 ...Pepsin catalytic domain / Aspartic peptidase, N-terminal / A1 Propeptide / 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 speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.34 Å
AuthorsCooper, J.B. / Khan, G. / Taylor, G. / Tickle, I.J. / Blundell, T.L.
CitationJournal: J.Mol.Biol. / Year: 1990
Title: X-ray analyses of aspartic proteinases. II. Three-dimensional structure of the hexagonal crystal form of porcine pepsin at 2.3 A resolution.
Authors: Cooper, J.B. / Khan, G. / Taylor, G. / Tickle, I.J. / Blundell, T.L.
History
DepositionMay 30, 1990Processing site: BNL
SupersessionJul 15, 1990ID: 2PEP
Revision 1.0Jul 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Nov 13, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PEPSIN


Theoretical massNumber of molelcules
Total (without water)34,4691
Polymers34,4691
Non-polymers00
Water6,684371
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.400, 67.400, 290.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Atom site foot note1: RESIDUE PRO 23 IS A CIS PROLINE.
2: REGIONS WITH HIGH THERMAL FACTORS ARE 240 - 245, 278 - 283, AND 294 - 298.
Components on special symmetry positions
IDModelComponents
11A-339-

HOH

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Components

#1: Protein PEPSIN


Mass: 34469.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P00791, pepsin A
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE OLD SEQUENCE FOR PORCINE PEPSIN HAD A RESIDUE AT POSITION 230 WHICH IS NOW KNOWN NOT TO EXIST. ...THE OLD SEQUENCE FOR PORCINE PEPSIN HAD A RESIDUE AT POSITION 230 WHICH IS NOW KNOWN NOT TO EXIST. THE OLD NUMBERING (228-229-231-232) HAS BEEN USED IN THIS ENTRY FOR HISTORICAL REASONS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.4 %
Crystal grow
*PLUS
pH: 3.6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1280 mg/mlenzyme 11
20.5 Msulphuric acid11

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Data collection

Reflection
*PLUS
Highest resolution: 2.34 Å / Num. obs: 15613 / Observed criterion σ(I): 3 / Num. measured all: 51501 / Rmerge(I) obs: 0.096

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Processing

SoftwareName: RESTRAIN / Classification: refinement
RefinementResolution: 2.34→10 Å / Rfactor obs: 0.196
Details: ISOTROPIC UISO VALUES ARE PROVIDED IN THE FIELD THAT USUALLY CONTAINS B VALUES. THERE IS NO APPARENT DENSITY FOR A PHOSPHATE COVALENTLY ATTACHED TO RESIDUE SER 68.
Refinement stepCycle: LAST / Resolution: 2.34→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2426 0 0 371 2797
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.022
X-RAY DIFFRACTIONp_angle_d0.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.34 Å / Lowest resolution: 10 Å / Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.4 Å / Num. reflection obs: 905 / Rfactor obs: 0.16

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