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- PDB-7ga9: PanDDA analysis group deposition -- Crystal Structure of MAP1LC3B... -

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Basic information

Entry
Database: PDB / ID: 7ga9
TitlePanDDA analysis group deposition -- Crystal Structure of MAP1LC3B in complex with Z1198177230
ComponentsMicrotubule-associated proteins 1A/1B light chain 3B
KeywordsSTRUCTURAL PROTEIN / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer
Function / homology
Function and homology information


SARS-CoV-2 modulates autophagy / ceramide binding / phosphatidylethanolamine binding / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs / cellular response to nitrogen starvation / Receptor Mediated Mitophagy / Macroautophagy / organelle membrane / autophagosome membrane ...SARS-CoV-2 modulates autophagy / ceramide binding / phosphatidylethanolamine binding / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs / cellular response to nitrogen starvation / Receptor Mediated Mitophagy / Macroautophagy / organelle membrane / autophagosome membrane / axoneme / autophagosome assembly / autophagosome maturation / mitophagy / endomembrane system / Pexophagy / autophagosome / cellular response to starvation / PINK1-PRKN Mediated Mitophagy / macroautophagy / mitochondrial membrane / autophagy / KEAP1-NFE2L2 pathway / Translation of Replicase and Assembly of the Replication Transcription Complex / cytoplasmic vesicle / microtubule binding / microtubule / ubiquitin protein ligase binding / mitochondrion / cytosol
Similarity search - Function
Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
: / Microtubule-associated protein 1 light chain 3 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 2.17 Å
AuthorsKumar, A. / Marples, P.G. / Tomlinson, C.W.E. / Fearon, D. / von-Delft, F. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)875510European Union
CitationJournal: To Be Published
Title: PanDDA analysis group deposition
Authors: Kumar, A. / Knapp, S. / Structural Genomics Consortium (SGC)
History
DepositionAug 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Microtubule-associated proteins 1A/1B light chain 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,00812
Polymers14,2371
Non-polymers77011
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.980, 60.980, 35.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Microtubule-associated proteins 1A/1B light chain 3B / Autophagy-related protein LC3 B / Autophagy-related ubiquitin-like modifier LC3 B / MAP1 light ...Autophagy-related protein LC3 B / Autophagy-related ubiquitin-like modifier LC3 B / MAP1 light chain 3-like protein 2 / MAP1A/MAP1B light chain 3 B / MAP1A/MAP1B LC3 B / Microtubule-associated protein 1 light chain 3 beta


Mass: 14237.361 Da / Num. of mol.: 1 / Mutation: TruncationafterGly120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP1LC3B, MAP1ALC3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GZQ8
#2: Chemical ChemComp-K6U / (2M)-2-(2-methoxyphenyl)-1,3,4-oxadiazole


Mass: 176.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.22 Å3/Da / Density % sol: 44.57 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.7 / Details: 36% PEG 8000, 0.1M acetate pH 4.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92124 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92124 Å / Relative weight: 1
ReflectionResolution: 2.17→30.49 Å / Num. obs: 7021 / % possible obs: 99.7 % / Redundancy: 13.3 % / CC1/2: 0.906 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.058 / Rrim(I) all: 0.208 / Net I/σ(I): 8.8 / Num. measured all: 93140 / Scaling rejects: 57
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.17-2.2313.33.30368725150.3530.9313.4330.998.4
9.71-30.499.80.063862880.9960.020.06724.397

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0267refinement
Aimless0.7.9data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 8Q53

8q53


Resolution: 2.17→30.51 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.938 / SU B: 9.866 / SU ML: 0.226 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.352 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2463 266 3.8 %RANDOM
Rwork0.1799 ---
obs0.1824 6749 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 156.73 Å2 / Biso mean: 56.978 Å2 / Biso min: 34.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å2-0 Å2-0 Å2
2--0.7 Å2-0 Å2
3----1.41 Å2
Refinement stepCycle: final / Resolution: 2.17→30.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms954 0 50 92 1096
Biso mean--83.33 67.7 -
Num. residues----113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0141343
X-RAY DIFFRACTIONr_bond_other_d0.0010.0141202
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.6671650
X-RAY DIFFRACTIONr_angle_other_deg1.2241.5812749
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9215156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.77419.42970
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.02915224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6791515
X-RAY DIFFRACTIONr_chiral_restr0.0610.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021423
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02313
X-RAY DIFFRACTIONr_mcbond_it3.8735.464622
X-RAY DIFFRACTIONr_mcbond_other3.875.462619
X-RAY DIFFRACTIONr_mcangle_it5.8878.192740
LS refinement shellResolution: 2.171→2.227 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 15 -
Rwork0.347 500 -
all-515 -
obs--98.28 %

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