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- PDB-1pci: PROCARICAIN -

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Basic information

Entry
Database: PDB / ID: 1pci
TitlePROCARICAIN
ComponentsPROCARICAIN
KeywordsTHIOL PROTEASE / ZYMOGEN / HYDROLASE
Function / homology
Function and homology information


caricain / cysteine-type peptidase activity / proteolysis
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesCarica papaya (papaya)
MethodX-RAY DIFFRACTION / SYNCHROTRON / COMBINED MOLECULAR REPLACEMENT, ISOMORPHOUS REPLACEMENT / Resolution: 3.2 Å
AuthorsGroves, M.R. / Taylor, M.A.J. / Scott, M. / Cummings, N.J. / Pickersgill, R.W. / Jenkins, J.A.
Citation
Journal: Structure / Year: 1996
Title: The prosequence of procaricain forms an alpha-helical domain that prevents access to the substrate-binding cleft.
Authors: Groves, M.R. / Taylor, M.A. / Scott, M. / Cummings, N.J. / Pickersgill, R.W. / Jenkins, J.A.
#1: Journal: Acta Crystallogr.,Sect.B / Year: 1991
Title: Determination of the Structure of Papaya Protease Omega
Authors: Pickersgill, R.W. / Rizkallah, P. / Harris, G.W. / Goodenough, P.W.
History
DepositionJun 28, 1996Processing site: BNL
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROCARICAIN
B: PROCARICAIN
C: PROCARICAIN


Theoretical massNumber of molelcules
Total (without water)107,8213
Polymers107,8213
Non-polymers00
Water0
1
A: PROCARICAIN


Theoretical massNumber of molelcules
Total (without water)35,9401
Polymers35,9401
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROCARICAIN


Theoretical massNumber of molelcules
Total (without water)35,9401
Polymers35,9401
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PROCARICAIN


Theoretical massNumber of molelcules
Total (without water)35,9401
Polymers35,9401
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.000, 205.400, 192.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.6866, 0.7268, 0.0167), (-0.727, 0.6866, 0.0092), (-0.0048, -0.0184, 0.9998)-133.9736, 98.6349, 35.2419
2given(-0.0165, 0.9999, -0.0026), (0.9996, 0.0165, -0.0212), (-0.0211, -0.003, -0.9998)-154.9361, 154.56219, 130.2691
DetailsTHE DEPOSITOR PROVIDED COORDINATES FOR CHAIN A. THE OTHER TWO CHAINS IN THE ASYMMETRIC UNIT WERE GENERATED BY THE PROTEIN DATA BANK USING THE MTRIX TRANSFORMATIONS BELOW.

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Components

#1: Protein PROCARICAIN / PRO PAPAYA PROTEASE OMEGA


Mass: 35940.328 Da / Num. of mol.: 3 / Mutation: H159G
Source method: isolated from a genetically manipulated source
Details: ACTIVE SITE HIS MUTATION / Source: (gene. exp.) Carica papaya (papaya) / Tissue: LEAF / Gene: OMEGA / Plasmid: PET3A / Gene (production host): OMEGA / Production host: Escherichia coli (E. coli) / References: UniProt: P10056, chymopapain
Source detailsPROCARICAIN IS A PLANT CYSTEINE PROTEASE FOUND IN THE LATEX OF CARICA PAPAYA.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 3.84 Å3/Da / Density % sol: 62 %
Crystal growpH: 7 / Details: pH 7.
Crystal grow
*PLUS
Temperature: 11 ℃ / pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15.5-8.5 mg/mlprotein1drop
275 mMsodium acetate1drop
31.5-1.7 Msodium formate1drop
40.05-0.1 Msodium chloride1drop
53.0-3.4 Msodium formate1reservoir
60.1-0.2 Msodium chloride1reservoir
70.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87, 1.0
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 23, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.871
211
ReflectionResolution: 3.2→96.2 Å / Num. obs: 27079 / % possible obs: 98.6 % / Observed criterion σ(I): 1 / Redundancy: 5.1 % / Biso Wilson estimate: 0.29 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 3.8
Reflection shellResolution: 3.21→3.34 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.169 / % possible all: 98.6
Reflection shell
*PLUS
% possible obs: 98.6 %

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Processing

Software
NameClassification
DENZOdata reduction
CCP4data reduction
DMmodel building
RAVEmodel building
X-PLORmodel building
X-PLORrefinement
CCP4data scaling
DMphasing
RAVEphasing
X-PLORphasing
RefinementMethod to determine structure: COMBINED MOLECULAR REPLACEMENT, ISOMORPHOUS REPLACEMENT
Starting model: MATURE CARICAIN (PDB ENTRY 1PPO)

1ppo


Resolution: 3.2→90.6 Å / Rfactor Rfree error: 0.0075 / Cross valid method: FREE R / σ(F): 1
Details: ELECTRON DENSITY FOR THE POLYPEPTIDE CHAIN 90P - 103P IS POOR. THE STRUCTURE WAS PRIMARILY MODELED IN THIS REGION. NCS RESTRAINTS WERE RELAXED FOR THE POLYPEPTIDE CHAIN 88P - 100P DUE TO NCS PACKING CLASHES.
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1451 3.001 %DATAMAN, SPHERICAL SHELLS
Rwork0.226 ---
obs0.226 27079 --
Displacement parametersBiso mean: 0.94 Å2
Baniso -1Baniso -2Baniso -3
1-16.8505 Å20 Å20 Å2
2---11.3966 Å20 Å2
3----5.4539 Å2
Refine analyzeLuzzati d res low obs: 96.2 Å
Refinement stepCycle: LAST / Resolution: 3.2→90.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3030 0 0 0 3030
Refine LS restraints NCSWeight Biso : 1 / Weight position: 300
LS refinement shellResolution: 3.2→3.22 Å / Rfactor Rfree error: 0.0072
RfactorNum. reflection% reflection
Rfree0.2772 15 2.96 %
Rwork0.3672 507 -
obs--98.6 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TPOH19.PEP
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 53.7 Å2

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