[English] 日本語
Yorodumi- PDB-2act: CRYSTALLOGRAPHIC REFINEMENT OF THE STRUCTURE OF ACTINIDIN AT 1.7 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2act | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CRYSTALLOGRAPHIC REFINEMENT OF THE STRUCTURE OF ACTINIDIN AT 1.7 ANGSTROMS RESOLUTION BY FAST FOURIER LEAST-SQUARES METHODS | |||||||||
Components | ACTINIDIN PRECURSOR | |||||||||
Keywords | HYDROLASE (PROTEINASE) | |||||||||
Function / homology | Function and homology information actinidain / proteolysis involved in protein catabolic process / lysosome / cysteine-type endopeptidase activity / extracellular space Similarity search - Function | |||||||||
Biological species | Actinidia chinensis (golden kiwifruit) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.7 Å | |||||||||
Authors | Baker, 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 |
| |||||||||
Remark 700 | SHEET 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2act.cif.gz | 57.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2act.ent.gz | 44.3 KB | Display | PDB format |
PDBx/mmJSON format | 2act.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2act_validation.pdf.gz | 420.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2act_full_validation.pdf.gz | 426.4 KB | Display | |
Data in XML | 2act_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 2act_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ac/2act ftp://data.pdbj.org/pub/pdb/validation_reports/ac/2act | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: 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. |
-Components
#1: Protein | 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 / |
#3: Water | ChemComp-HOH / |
Nonpolymer details | ALL 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 RELIABILIT |
Sequence details | AMINO ACID SEQUENCE ANALYSIS IDENTIFIES RESIDUE 86 AS ASP, BUT REFINEMENT SHOWS IT TO BE GLN OR GLU ...AMINO ACID SEQUENCE ANALYSIS IDENTIFIES |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.83 % |
---|---|
Crystal grow | *PLUS Method: other / Details: Baker, E.N., (1974) J. Mol. Bol., 74, 411. |
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.7 Å / Num. obs: 24157 / Num. measured all: 47000 / Rmerge(I) obs: 0.056 |
-Processing
Software | Name: FAST-FOURIER / Version: LEAST-SQUARES REFINEMENT / Classification: refinement | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 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.
| ||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→10 Å
| ||||||||||||
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 |