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

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Basic information

Entry
Database: PDB / ID: 7gab
TitlePanDDA analysis group deposition -- Crystal Structure of MAP1LC3B in complex with Z1255402624
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 / autophagy of mitochondrion / cellular response to nitrogen starvation / TBC/RABGAPs / Receptor Mediated Mitophagy / organelle membrane / Macroautophagy ...SARS-CoV-2 modulates autophagy / ceramide binding / phosphatidylethanolamine binding / Translation of Replicase and Assembly of the Replication Transcription Complex / autophagy of mitochondrion / cellular response to nitrogen starvation / TBC/RABGAPs / Receptor Mediated Mitophagy / organelle membrane / Macroautophagy / axoneme / autophagosome membrane / autophagosome maturation / autophagosome assembly / mitophagy / endomembrane system / autophagosome / Pexophagy / 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 / intracellular membrane-bounded organelle / 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
2-tert-butylbenzene-1,4-diol / Microtubule-associated proteins 1A/1B light chain 3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 2.23 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)14,99812
Polymers14,2371
Non-polymers76011
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)60.892, 60.892, 35.588
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-EYK / 2-tert-butylbenzene-1,4-diol


Mass: 166.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14O2 / 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: 2.23 Å3/Da / Density % sol: 44.83 % / 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: 2.23→43.05 Å / Num. obs: 6512 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.041 / Rrim(I) all: 0.15 / Net I/σ(I): 10.3 / Num. measured all: 87203 / Scaling rejects: 0
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
2.23-2.3113.43.60378545840.2791.0223.7470.5100
8.93-43.0510.50.05212231160.990.0170.05544.699.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0267refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 8Q53

8q53


Resolution: 2.23→43.09 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.921 / SU B: 15.017 / SU ML: 0.328 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.45 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2755 251 3.9 %RANDOM
Rwork0.1868 ---
obs0.1902 6243 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 186.99 Å2 / Biso mean: 66.317 Å2 / Biso min: 34.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å2-0 Å2-0 Å2
2--0.39 Å2-0 Å2
3----0.77 Å2
Refinement stepCycle: final / Resolution: 2.23→43.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms954 0 49 92 1095
Biso mean--98.23 71.67 -
Num. residues----113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0141338
X-RAY DIFFRACTIONr_bond_other_d0.0010.0141217
X-RAY DIFFRACTIONr_angle_refined_deg1.6251.6671650
X-RAY DIFFRACTIONr_angle_other_deg1.2191.5822767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.725156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.90819.42970
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.73815224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1011515
X-RAY DIFFRACTIONr_chiral_restr0.0740.2154
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021413
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02309
X-RAY DIFFRACTIONr_mcbond_it5.3656.375622
X-RAY DIFFRACTIONr_mcbond_other5.376.373619
X-RAY DIFFRACTIONr_mcangle_it8.1659.575740
LS refinement shellResolution: 2.233→2.291 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 17 -
Rwork0.352 450 -
all-467 -
obs--98.94 %

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