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- PDB-3vx6: Crystal structure of Kluyveromyces marxianus Atg7NTD -

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Basic information

Entry
Database: PDB / ID: 3vx6
TitleCrystal structure of Kluyveromyces marxianus Atg7NTD
ComponentsE1
KeywordsLIGASE / E2 binding / E1
Function / homologyUbiquitin-like modifier-activating enzyme Atg7, N-terminal / Ubiquitin-like modifier-activating enzyme Atg7, N-terminal, subdomain 1 / Ubiquitin-like modifier-activating enzyme Atg7, N-terminal, subdomain 2 / Ubiquitin-like modifier-activating enzyme ATG7 N-terminus / E1
Function and homology information
Biological speciesKluyveromyces marxianus (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYamaguchi, M. / Matoba, K. / Sawada, R. / Fujioka, Y. / Nakatogawa, H. / Yamamoto, H. / Kobashigawa, Y. / Hoshida, H. / Akada, R. / Ohsumi, Y. ...Yamaguchi, M. / Matoba, K. / Sawada, R. / Fujioka, Y. / Nakatogawa, H. / Yamamoto, H. / Kobashigawa, Y. / Hoshida, H. / Akada, R. / Ohsumi, Y. / Noda, N.N. / Inagaki, F.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Noncanonical recognition and UBL loading of distinct E2s by autophagy-essential Atg7.
Authors: Yamaguchi, M. / Matoba, K. / Sawada, R. / Fujioka, Y. / Nakatogawa, H. / Yamamoto, H. / Kobashigawa, Y. / Hoshida, H. / Akada, R. / Ohsumi, Y. / Noda, N.N. / Inagaki, F.
History
DepositionSep 11, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 8, 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: E1


Theoretical massNumber of molelcules
Total (without water)32,2141
Polymers32,2141
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: E1

A: E1


Theoretical massNumber of molelcules
Total (without water)64,4282
Polymers64,4282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area1320 Å2
ΔGint-9 kcal/mol
Surface area23580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.908, 118.908, 45.050
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein E1


Mass: 32213.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces marxianus (yeast) / Plasmid: pGBHPS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: L7MTK3*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 2.85 Å3/Da / Density % sol: 56.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 2.0M ammonium sulfate, 0.2M potassium/sodium tartrate, 0.1M citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 24, 2011
RadiationMonochromator: Rotated-inclined double-crystal monochromator , Si (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→38.92 Å / Num. all: 12559 / Num. obs: 12144 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 20 % / Biso Wilson estimate: 62.1 Å2 / Rsym value: 0.065 / Net I/σ(I): 19.2
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 19.6 % / Mean I/σ(I) obs: 8.6 / Num. unique all: 1251 / Rsym value: 0.3 / % possible all: 67

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VH1

3vh1


Resolution: 2.6→38.92 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 97156.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1168 10.3 %RANDOM
Rwork0.224 ---
all0.228 ---
obs0.224 11354 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.4125 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 49.7 Å2
Baniso -1Baniso -2Baniso -3
1-4.98 Å20 Å20 Å2
2--4.98 Å20 Å2
3----9.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.6→38.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2113 0 0 17 2130
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it2.172
X-RAY DIFFRACTIONc_scbond_it1.772
X-RAY DIFFRACTIONc_scangle_it2.722.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.347 193 10.8 %
Rwork0.303 1600 -
obs-1793 94.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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