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- PDB-1am5: THE CRYSTAL STRUCTURE AND PROPOSED AMINO ACID SEQUENCE OF A PEPSI... -

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Basic information

Entry
Database: PDB / ID: 1am5
TitleTHE CRYSTAL STRUCTURE AND PROPOSED AMINO ACID SEQUENCE OF A PEPSIN FROM ATLANTIC COD (GADUS MORHUA)
ComponentsPEPSIN
KeywordsASPARTYL PROTEASE / ACID PROTEINASE / HYDROLASE
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / digestion / aspartic-type endopeptidase activity
Similarity search - Function
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 speciesGadus morhua (Atlantic cod)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsKarlsen, S. / Hough, E. / Olsen, R.L.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structure and proposed amino-acid sequence of a pepsin from atlantic cod (Gadus morhua).
Authors: Karlsen, S. / Hough, E. / Olsen, R.L.
#1: Journal: COMP.BIOCHEM.PHYSIOL. B: BIOCHEM.MOL.BIOL. / Year: 1990
Title: Catalytic Properties and Chemical Composition of Pepsins from Atlantic Cod (Gadus Morhua)
Authors: Gildberg, A. / Olsen, R.L. / Bjarnason, J.B.
History
DepositionJun 23, 1997Processing site: BNL
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.4Aug 2, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)34,0341
Polymers34,0341
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.980, 75.400, 108.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PEPSIN / ACID PROTEINASE


Mass: 34033.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gadus morhua (Atlantic cod) / Organ: STOMACH / Tissue: GASTRIC MUCOSA / References: UniProt: P56272, pepsin A
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AMINO ACID NUMBERING IS BASED ON THE SEQUENCE OF PEPSIN FROM PORCINE. AS RESIDUE 207 AND 241 ...THE AMINO ACID NUMBERING IS BASED ON THE SEQUENCE OF PEPSIN FROM PORCINE. AS RESIDUE 207 AND 241 NOT ARE PRESENT IN THE COD PEPSIN, THESE RESIDUES ARE DELETED IN THE COORDINATE FILE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 43 %
Crystal growpH: 5.4 / Details: 7.5 % 2-PROPANOL, 100 MM SODIUM ACETATE PH 5.4
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
23.75 %2-propanol1drop
350 mMsodium acetate1drop
47.5 %2-propanol1reservoir
5100 mM2-propanol1reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceType: BRUKER NONIUS / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Oct 1, 1995 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.16→20 Å / Num. obs: 13687 / % possible obs: 83.7 % / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Biso Wilson estimate: 22.3 Å2 / Rsym value: 0.066 / Net I/σ(I): 10.8
Reflection shellResolution: 2.16→2.28 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.221 / % possible all: 41.4
Reflection
*PLUS
Num. measured all: 37108 / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 41.4 % / Num. unique obs: 948 / Num. measured obs: 1322 / Rmerge(I) obs: 0.221

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Processing

Software
NameClassification
MADNESdata collection
CCP4data reduction
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
MADNESdata reduction
CCP4data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5PEP

5pep


Resolution: 2.16→8 Å / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.224 -5 %RANDOM
Rwork0.208 ---
obs-13315 --
Displacement parametersBiso mean: 17.22 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.16→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2395 0 0 161 2556
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.071
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.091
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_restr0.196
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
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS

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