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- PDB-3psg: THE HIGH RESOLUTION CRYSTAL STRUCTURE OF PORCINE PEPSINOGEN -

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Basic information

Entry
Database: PDB / ID: 3psg
TitleTHE HIGH RESOLUTION CRYSTAL STRUCTURE OF PORCINE PEPSINOGEN
ComponentsPEPSINOGEN
KeywordsHYDROLASE(ACID PROTEINASE ZYMOGEN)
Function / homology
Function and homology information


Surfactant metabolism / pepsin A / digestion / aspartic-type endopeptidase activity / proteolysis / extracellular exosome
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: 1.65 Å
AuthorsHartsuck, J.A. / Koelsch, G. / Remington, S.J.
CitationJournal: Proteins / Year: 1992
Title: The high-resolution crystal structure of porcine pepsinogen.
Authors: Hartsuck, J.A. / Koelsch, G. / Remington, S.J.
History
DepositionSep 3, 1991Processing site: BNL
SupersessionJan 15, 1993ID: 1PSG
Revision 1.0Jan 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Remark 650HELIX A NUMBER OF BETA TURNS ARE ALSO LISTED AS 3/10 HELICES, WHERE APPROPRIATE.
Remark 700SHEET ONE OF THE SHEETS IN THIS ENTRY (SHEET S2), CONTAINING SIX STRANDS, IS A BETA BARREL ...SHEET ONE OF THE SHEETS IN THIS ENTRY (SHEET S2), CONTAINING SIX STRANDS, IS A BETA BARREL CONTAINING AN EXTENSION COMPRISED OF RESIDUES 65 - 90 WHICH FORMS A SECOND HYDROPHOBIC CORE WITH THE SURFACE OF THE BARREL. THIS IS REPRESENTED IN THIS ENTRY BY A SEVEN-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. ADDITIONALLY, THE THIRD STRAND IS COMPOSED OF THREE NONCONTIGUOUS FRAGMENTS (RESIDUES 16 - 20, 65 - 67, AND 69 - 75). THIS IS REPRESENTED BY DESCRIBING THE SHEET THREE TIMES (SHEETS *S2A*, *S2B*, AND *S2C* BELOW) WITH DIFFERENT THIRD STRANDS. REGISTRATION INFORMATION IS NOT INCLUDED WHEN TWO ADJACENT STRANDS DO NOT INTERACT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEPSINOGEN


Theoretical massNumber of molelcules
Total (without water)39,5521
Polymers39,5521
Non-polymers00
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.100, 43.700, 88.900
Angle α, β, γ (deg.)90.00, 91.40, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: RESIDUE PRO 23 IS A CIS PROLINE.

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Components

#1: Protein PEPSINOGEN


Mass: 39551.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P00791
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPROPEPTIDE RESIDUES HAVE BEEN ASSIGNED INSERTION CODE P AND NUMBERED FROM 1 TO 44. THE REMAINDER OF ...PROPEPTIDE RESIDUES HAVE BEEN ASSIGNED INSERTION CODE P AND NUMBERED FROM 1 TO 44. THE REMAINDER OF THE RESIDUES ARE NUMBERED FROM 1 TO 326.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.75 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.1 / Method: batch method / Details: crystalyzed by either batch or vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.95 %protein11
252 %satlithium sulfate11
30.025 Msodium cacodylate11

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Data collection

Reflection
*PLUS
Highest resolution: 1.65 Å / Num. obs: 31236 / Num. measured all: 68120 / Rmerge F obs: 0.082
Reflection shell
*PLUS
Highest resolution: 1.65 Å / Lowest resolution: 1.75 Å / % possible obs: 18.4 %

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Processing

SoftwareName: TNT / Classification: refinement
RefinementRfactor obs: 0.17 / Highest resolution: 1.65 Å
Details: RESIDUE SER 68 IS PHOSPHORYLATED BUT THE SIDE CHAIN DENSITY IS SO WEAK THAT ONLY CB HAS BEEN INCLUDED.
Refinement stepCycle: LAST / Highest resolution: 1.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2692 0 0 180 2872
Software
*PLUS
Name: 'TNT, EREF' / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / Num. reflection obs: 28806 / σ(F): 1.3 / Rfactor obs: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.014
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg2.6
X-RAY DIFFRACTIONo_dihedral_angle_d

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