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- PDB-2act: CRYSTALLOGRAPHIC REFINEMENT OF THE STRUCTURE OF ACTINIDIN AT 1.7 ... -

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Basic information

Entry
Database: PDB / ID: 2act
TitleCRYSTALLOGRAPHIC REFINEMENT OF THE STRUCTURE OF ACTINIDIN AT 1.7 ANGSTROMS RESOLUTION BY FAST FOURIER LEAST-SQUARES METHODS
ComponentsACTINIDIN PRECURSOR
KeywordsHYDROLASE (PROTEINASE)
Function / homology
Function and homology information


actinidain / proteolysis involved in protein catabolic process / lysosome / cysteine-type endopeptidase activity / extracellular space
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
AMMONIUM ION / Actinidain
Similarity search - Component
Biological speciesActinidia chinensis (golden kiwifruit)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsBaker, E.N.
Citation
Journal: Acta Crystallogr.,Sect.A / Year: 1980
Title: Crystallographic Refinement of the Structure of Actinidin at 1.7 Angstroms Resolution by Fast Fourier Least-Squares Methods
Authors: Baker, E.N. / Dodson, E.J.
#1: Journal: J.Mol.Biol. / Year: 1980
Title: Structure of Actinidin, After Refinement at 1.7 Angstroms Resolution
Authors: Baker, E.N.
#2: Journal: J.Mol.Biol. / Year: 1977
Title: Structure of Actinidin. Details of the Polypeptide Chain Conformation and Active Site from an Electron Density Map at 2.8 Angstroms Resolution
Authors: Baker, E.N.
#3: Journal: Biochem.J. / Year: 1978
Title: The Amino Acid Sequence of the Tryptic Peptides from Actinidin, a Proteolytic Enzyme from the Fruit of Actinidia Chinensis
Authors: Carne, A. / Moore, C.H.
History
DepositionNov 27, 1979Processing site: BNL
SupersessionMar 7, 1980ID: 1ACT
Revision 1.0Mar 7, 1980Provider: 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
Remark 700SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE ...SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. STRANDS 2, 3, 4, 5 OF B1 AND B2 ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACTINIDIN PRECURSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7372
Polymers23,7191
Non-polymers181
Water4,900272
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.200, 81.800, 33.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES 9, 42, 44, 58 AND 129 ARE DISORDERED. / 2: SEE REMARK 10.
3: AMINO ACID SEQUENCE ANALYSIS IDENTIFIES RESIDUE 86 AS ASP, BUT REFINEMENT SHOWS IT TO BE GLN OR GLU (HERE TAKEN AS GLU).
4: NO DENSITY BEYOND CB. / 5: POORLY DEFINED BEYOND CB.
6: ELECTRON DENSITY PEAK 2 ANGSTROMS FROM CB. COULD BE SER (I.E. SEQUENCE ERROR). PEAK CURRENTLY IDENTIFIED AS HOH 92.
7: POORLY DEFINED SIDECHAIN. / 8: CIS-PROLINE.
9: REFINED POORLY. COULD BE SEQUENCE ERROR. SHOULD PERHAPS BE VAL.
10: VERY WEAK DENSITY.

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Components

#1: Protein ACTINIDIN PRECURSOR


Mass: 23718.986 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinidia chinensis (golden kiwifruit) / References: UniProt: P00785
#2: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsALL SOLVENT MOLECULES ARE REGARDED AS WATER, WITH THE EXCEPTION OF NH4 4 WHICH IS BELIEVED TO BE AN ...ALL SOLVENT MOLECULES ARE REGARDED AS WATER, WITH THE EXCEPTION OF NH4 4 WHICH IS BELIEVED TO BE AN AMMONIUM ION AND HAS THREE HYDROGEN-BOND ACCEPTORS AS NEAREST NEIGHBORS. SOLVENT MOLECULES ARE NUMBERED IN ORDER OF THEIR RELIABILITY (BASED ON B VALUES). HOH 1 TO HOH 163 HAVE BEEN REFINED. HOH 164 TO HOH 273 HAVE BEEN ADDED FOLLOWING A FINAL DIFFERENCE MAP AND NOT REFINED. THEY ARE LESS RELIABLE AND LESS ORDERED.
Sequence detailsAMINO ACID SEQUENCE ANALYSIS IDENTIFIES RESIDUE 86 AS ASP, BUT REFINEMENT SHOWS IT TO BE GLN OR GLU ...AMINO ACID SEQUENCE ANALYSIS IDENTIFIES RESIDUE 86 AS ASP, BUT REFINEMENT SHOWS IT TO BE GLN OR GLU (HERE TAKEN AS GLU)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.83 %
Crystal grow
*PLUS
Method: other / Details: Baker, E.N., (1974) J. Mol. Bol., 74, 411.

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.7 Å / Num. obs: 24157 / Num. measured all: 47000 / Rmerge(I) obs: 0.056

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Processing

SoftwareName: FAST-FOURIER / Version: LEAST-SQUARES REFINEMENT / Classification: refinement
RefinementResolution: 1.7→10 Å
Details: ACCURACY OF ATOMIC COORDINATES (DERIVED FROM INVERSE LEAST-SQUARES MATRIX) IS GIVEN BELOW AS A FUNCTION OF ATOMIC B VALUE. B(ANGSTROMS SQUARED) SIGMA 0 - 5 0.04 ANGSTROMS 5 - 10 0.05 ...Details: ACCURACY OF ATOMIC COORDINATES (DERIVED FROM INVERSE LEAST-SQUARES MATRIX) IS GIVEN BELOW AS A FUNCTION OF ATOMIC B VALUE. B(ANGSTROMS SQUARED) SIGMA 0 - 5 0.04 ANGSTROMS 5 - 10 0.05 ANGSTROMS 10 - 15 0.06 ANGSTROMS 15 - 20 0.07 ANGSTROMS OVER 20 0.08 ANGSTROMS OVERALL 0.06 ANGSTROMS ATOMS IN ASN AND GLN SIDE CHAINS ARE LABELLED AS OD1 AND ND2 OR OE1 AND NE2 RESPECTIVELY, THE CHOICE BEING BASED ON ENVIRONMENT (E.G. H-BONDS) AND/OR B VALUES.
RfactorNum. reflection
Rwork0.171 -
obs-23990
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1647 0 1 272 1920
Refinement
*PLUS
Num. reflection all: 23990 / Num. reflection obs: 19724 / σ(I): 2 / Rfactor all: 0.171 / Rfactor obs: 0.152
Solvent computation
*PLUS
Displacement parameters
*PLUS

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