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- PDB-2d1i: Structure of human Atg4b -

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Basic information

Entry
Database: PDB / ID: 2d1i
TitleStructure of human Atg4b
ComponentsCysteine protease APG4B
KeywordsHYDROLASE / CYSTEINE PROTEASE / AUTOPHAGY / ATG / APG
Function / homology
Function and homology information


protein-phosphatidylethanolamide deconjugating activity / otolith mineralization completed early in development / protein delipidation / microautophagy / protein localization to phagophore assembly site / Macroautophagy / autophagosome membrane / mitophagy / autophagosome assembly / cysteine-type peptidase activity ...protein-phosphatidylethanolamide deconjugating activity / otolith mineralization completed early in development / protein delipidation / microautophagy / protein localization to phagophore assembly site / Macroautophagy / autophagosome membrane / mitophagy / autophagosome assembly / cysteine-type peptidase activity / macroautophagy / autophagy / protein transport / cytoplasmic vesicle / scaffold protein binding / endopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type endopeptidase activity / endoplasmic reticulum / mitochondrion / proteolysis / cytosol
Similarity search - Function
Peptidase C54, catalytic domain / Cysteine protease ATG4, F-type LIR motif / ATG4, F-type LIR motif / Peptidase C54 / Peptidase family C54 / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Cysteine protease ATG4B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsKumanomidou, T. / Mizushima, T. / Komatsu, M. / Suzuki, A. / Tanida, I. / Sou, Y.S. / Ueno, T. / Kominami, E. / Tanaka, K. / Yamane, T.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: The Crystal Structure of Human Atg4b, a Processing and De-conjugating Enzyme for Autophagosome-forming Modifiers
Authors: Kumanomidou, T. / Mizushima, T. / Komatsu, M. / Suzuki, A. / Tanida, I. / Sou, Y.S. / Ueno, T. / Kominami, E. / Tanaka, K. / Yamane, T.
History
DepositionAug 24, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 10, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteine protease APG4B
B: Cysteine protease APG4B


Theoretical massNumber of molelcules
Total (without water)89,5292
Polymers89,5292
Non-polymers00
Water6,089338
1
A: Cysteine protease APG4B


Theoretical massNumber of molelcules
Total (without water)44,7651
Polymers44,7651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cysteine protease APG4B


Theoretical massNumber of molelcules
Total (without water)44,7651
Polymers44,7651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.278, 161.321, 51.271
Angle α, β, γ (deg.)90.00, 119.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cysteine protease APG4B / Autophagy 4 homolog B / hAPG4B / Autophagin-1 / Autophagy-related cysteine endopeptidase 1 / AUT- ...Autophagy 4 homolog B / hAPG4B / Autophagin-1 / Autophagy-related cysteine endopeptidase 1 / AUT-like 1 cysteine endopeptidase / Atg4b


Mass: 44764.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX6P / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9Y4P1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 7

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 40.4 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.65M tri-Sodium citrate dihydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Oct 9, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→44.59 Å / Num. obs: 48166 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 33.018 Å2
Reflection shellResolution: 2→2.07 Å / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 2→44.59 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.908 / SU B: 4.916 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28317 2435 5.1 %RANDOM
Rwork0.22033 ---
all0.22351 45690 --
obs0.22351 45690 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.978 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20.06 Å2
2---0.22 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 2→44.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5386 0 0 338 5724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225538
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.9517528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0855674
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55223.651252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.78915900
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8191534
X-RAY DIFFRACTIONr_chiral_restr0.0970.2812
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024246
X-RAY DIFFRACTIONr_nbd_refined0.2220.22726
X-RAY DIFFRACTIONr_nbtor_refined0.3080.23779
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2388
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.2119
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.229
X-RAY DIFFRACTIONr_mcbond_it0.9551.53467
X-RAY DIFFRACTIONr_mcangle_it1.64825488
X-RAY DIFFRACTIONr_scbond_it1.81632379
X-RAY DIFFRACTIONr_scangle_it2.8384.52040
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 199 -
Rwork0.246 3411 -
obs--98.88 %

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