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- PDB-2psg: REFINED STRUCTURE OF PORCINE PEPSINOGEN AT 1.8 ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 2psg
TitleREFINED STRUCTURE OF PORCINE PEPSINOGEN AT 1.8 ANGSTROMS RESOLUTION
ComponentsPEPSINOGEN
KeywordsHYDROLASE(ACID PROTEINASE ZYMOGEN)
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: 1.8 Å
AuthorsJames, M.N.G. / Sielecki, A.R.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: Refined structure of porcine pepsinogen at 1.8 A resolution.
Authors: Sielecki, A.R. / Fujinaga, M. / Read, R.J. / James, M.N.
#1: Journal: Nature / Year: 1986
Title: Molecular Structure of an Aspartic Proteinase Zymogen, Porcine Pepsinogen, at 1.8 Angstroms Resolution
Authors: James, M.N.G. / Sielecki, A.R.
#2: Journal: Biochemistry / Year: 1986
Title: Characterization of Phosphoserine of Pepsinogen Using 31P Nuclear Magnetic Resonance: Corroboration of X-Ray Crystallographic Results
Authors: Williams, S.P. / Bridger, W.A. / James, M.N.G.
History
DepositionJan 23, 1991Processing site: BNL
Revision 1.0Oct 15, 1992Provider: 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 ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif / struct_sheet
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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_sheet.number_strands
Revision 1.4Oct 16, 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

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Assembly

Deposited unit
A: PEPSINOGEN


Theoretical massNumber of molelcules
Total (without water)39,6321
Polymers39,6321
Non-polymers00
Water4,270237
1
A: PEPSINOGEN

A: PEPSINOGEN


Theoretical massNumber of molelcules
Total (without water)79,2632
Polymers79,2632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)105.780, 43.410, 88.580
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.
2: RESIDUE SER 68 IS PHOSHORYLATED. THE PHOSPHATE GROUP IS PRESENTED AS HET GROUP PO3 ON HET RECORDS AT THE END OF THE CHAIN.
Components on special symmetry positions
IDModelComponents
11A-371-

HOH

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Components

#1: Protein PEPSINOGEN


Mass: 39631.504 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.: 237 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE USED IN THIS ENTRY IS THAT OF P.SEPULVEDA, J.MARCINISZYN JR.,D.LIU,J.TANG (J.BIO.CHEM. ...THE SEQUENCE USED IN THIS ENTRY IS THAT OF P.SEPULVEDA, J.MARCINISZYN JR.,D.LIU,J.TANG (J.BIO.CHEM.,V.250,P.5082, 1975). NOTE THAT THIS SEQUENCE DIFFERS FROM THAT IN PROTEIN IDENTIFICATION RESOURCE (PIR) ENTRY PEPG. IN PIR ENTRY PEPG RESIDUE 263 IS IDENTIFIED AS ASN WHILE IN THE JBC PAPER AND IN THIS ENTRY RESIDUE 263 IS IDENTIFIED AS ASP.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.05 %
Crystal grow
*PLUS
pH: 6.1 / Method: vapor diffusion, hanging drop / Details: took James & Sielecki, 1986 from original paper
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
21.8 M1reserviorLi2SO4
350 mM[N-morpholino]ethane sulphonic acid1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 40 Å / Num. obs: 27251 / Observed criterion σ(I): 2 / Num. measured all: 37575 / Rmerge(I) obs: 0.058

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→8 Å / σ(I): 1 /
RfactorNum. reflection
obs0.164 32264
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2794 0 0 237 3031
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d0.047
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.048
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.4
X-RAY DIFFRACTIONp_mcangle_it3.6
X-RAY DIFFRACTIONp_scbond_it3.9
X-RAY DIFFRACTIONp_scangle_it5.6
X-RAY DIFFRACTIONp_plane_restr0.008
X-RAY DIFFRACTIONp_chiral_restr0.179
X-RAY DIFFRACTIONp_singtor_nbd0.251
X-RAY DIFFRACTIONp_multtor_nbd0.183
X-RAY DIFFRACTIONp_xhyhbond_nbd0.173
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor1.6
X-RAY DIFFRACTIONp_staggered_tor16
X-RAY DIFFRACTIONp_orthonormal_tor20
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.164
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15 Å2

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