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- PDB-4pep: THE MOLECULAR AND CRYSTAL STRUCTURES OF MONOCLINIC PORCINE PEPSIN... -

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Basic information

Entry
Database: PDB / ID: 4pep
TitleTHE MOLECULAR AND CRYSTAL STRUCTURES OF MONOCLINIC PORCINE PEPSIN REFINED AT 1.8 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: 1.8 Å
AuthorsAndreeva, N. / Fedorov, A.A. / Sielecki, A. / James, M.
CitationJournal: J.Mol.Biol. / Year: 1990
Title: Molecular and crystal structures of monoclinic porcine pepsin refined at 1.8 A resolution.
Authors: Sielecki, A.R. / Fedorov, A.A. / Boodhoo, A. / Andreeva, N.S. / James, M.N.
History
DepositionDec 18, 1989Processing site: BNL
SupersessionApr 15, 1990ID: 1PEP
Revision 1.0Apr 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 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 700SHEET THE SHEET IDENTIFIED AS *I* BY THE DEPOSITORS CONTAINS A BIFURCATED STRAND. THIS IS ...SHEET THE SHEET IDENTIFIED AS *I* BY THE DEPOSITORS CONTAINS A BIFURCATED STRAND. THIS IS REPRESENTED BY DEFINING THE SHEET TWICE ON *SHEET* RECORDS BELOW. THUS SHEETS *IA* *IB* DIFFER ONLY IN STRAND 6.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEPSIN


Theoretical massNumber of molelcules
Total (without water)34,5941
Polymers34,5941
Non-polymers00
Water3,369187
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.830, 36.440, 73.680
Angle α, β, γ (deg.)90.00, 103.80, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUE PRO 23 IS A CIS PROLINE.
2: AS DETAILED IN THE REFERENCE CITED ON THE *JRNL* RECORDS ABOVE, THE FOLLOWING LOOPS ARE POORLY DETERMINED IN THE STRUCTURE PRESENTED IN THIS ENTRY (B FACTORS .GT. 40A**2) -ASP 200 - THR 203 SER ...2: AS DETAILED IN THE REFERENCE CITED ON THE *JRNL* RECORDS ABOVE, THE FOLLOWING LOOPS ARE POORLY DETERMINED IN THE STRUCTURE PRESENTED IN THIS ENTRY (B FACTORS .GT. 40A**2) -ASP 200 - THR 203 SER 241 - GLY 243 SER 250 - ASP 253 GLN 277 - SER 281 ASP 290 - GLU 297 IN ADDITION, THE SIDE CHAINS OF RESIDUES LEU 166 AND GLU 244 - ILE 247 HAVE POORLY DEFINED ELECTRON DENSITY AND/OR COULD HAVE MORE THAN ONE POSSIBLE CONFORMATION.

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Components

#1: Protein PEPSIN


Mass: 34594.469 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.: 187 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.47 %
Crystal grow
*PLUS
pH: 2 / Method: other / Details: pH is adjusted to 2.0 with 1M H2SO4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlpepsin11
220 %(v/v)ethanol11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 23897 / Num. measured all: 90730 / Rmerge(I) obs: 0.062

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→8 Å / σ(F): 3
Details: 187 SOLVENTS ARE INCLUDED IN THIS ENTRY (HOH 328 TO 514). THOSE WITH LOWER RESIDUE NUMBERS (LOWER B FACTORS, HIGHER OCCUPANCIES) ARE MORE RELIABLE THAN THOSE LOCATED TOWARDS THE END OF THE ...Details: 187 SOLVENTS ARE INCLUDED IN THIS ENTRY (HOH 328 TO 514). THOSE WITH LOWER RESIDUE NUMBERS (LOWER B FACTORS, HIGHER OCCUPANCIES) ARE MORE RELIABLE THAN THOSE LOCATED TOWARDS THE END OF THE LIST (HIGHER B FACTORS, LOWER OCCUPANCIES).
RfactorNum. reflection
all0.189 23567
obs0.174 20519
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2433 0 0 187 2620
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.024
X-RAY DIFFRACTIONp_angle_d0.0480.048
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0440.048
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.31.5
X-RAY DIFFRACTIONp_mcangle_it4.12
X-RAY DIFFRACTIONp_scbond_it4.92.5
X-RAY DIFFRACTIONp_scangle_it63
X-RAY DIFFRACTIONp_plane_restr0.0080.014
X-RAY DIFFRACTIONp_chiral_restr0.1840.15
X-RAY DIFFRACTIONp_singtor_nbd0.240.4
X-RAY DIFFRACTIONp_multtor_nbd0.1920.4
X-RAY DIFFRACTIONp_xhyhbond_nbd0.215
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor1.76
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
σ(F): 3 / Highest resolution: 1.8 Å / Lowest resolution: 8 Å / Num. reflection obs: 20519 / Rfactor obs: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS

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