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- PDB-3p5u: Actinidin from Actinidia arguta planch (Sarusashi) -

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Basic information

Entry
Database: PDB / ID: 3p5u
TitleActinidin from Actinidia arguta planch (Sarusashi)
ComponentsActinidinActinidain
KeywordsHYDROLASE / SAD / Cysteine proteinases
Function / homology
Function and homology information


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 speciesActinidia arguta (plant)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.5 Å
AuthorsManickam, Y. / Nirmal, N. / Suzuki, A. / Sugiyama, Y. / Yamane, T. / Devadasan, V. / Sharma, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Structural analysis of actinidin and a comparison of cadmium and sulfur anomalous signals from actinidin crystals measured using in-house copper- and chromium-anode X-ray sources
Authors: Yogavel, M. / Nithya, N. / Suzuki, A. / Sugiyama, Y. / Yamane, T. / Velmurugan, D. / Sharma, A.
History
DepositionOct 11, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Actinidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5716
Polymers24,0091
Non-polymers5625
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.786, 56.178, 70.881
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Actinidin / Actinidain


Mass: 24009.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Actinidia arguta (plant) / References: UniProt: A5HII2*PLUS, actinidain
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE DEPOSITED IN THE SEQUENCE DATABASE.

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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: 2.02 Å3/Da / Density % sol: 39.19 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 30% PEG 400, 0.1M sodium acetate, 30mM Cadmium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 15, 2008
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→110 Å / Num. obs: 31698 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 45.4
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 9.64 / % possible all: 98.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SOLVEphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.5→18.42 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.2255 / WRfactor Rwork: 0.2021 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8711 / SU B: 1.289 / SU ML: 0.05 / SU R Cruickshank DPI: 0.0864 / SU Rfree: 0.0831 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2086 1599 5 %RANDOM
Rwork0.1851 ---
obs0.1864 31690 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.08 Å2 / Biso mean: 17.1737 Å2 / Biso min: 8.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2---0.08 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.5→18.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1690 0 5 288 1983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221793
X-RAY DIFFRACTIONr_angle_refined_deg0.8871.9242458
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.945237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84425.66790
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.05215266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.03155
X-RAY DIFFRACTIONr_chiral_restr0.0630.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021427
X-RAY DIFFRACTIONr_nbd_refined0.2010.2891
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21253
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0830.2251
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0660.228
X-RAY DIFFRACTIONr_mcbond_it0.3741.51147
X-RAY DIFFRACTIONr_mcangle_it0.67121791
X-RAY DIFFRACTIONr_scbond_it13772
X-RAY DIFFRACTIONr_scangle_it1.4224.5658
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 100 -
Rwork0.335 2183 -
all-2283 -
obs--97.73 %

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