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

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Basic information

Entry
Database: PDB / ID: 7gaf
TitlePanDDA analysis group deposition -- Crystal Structure of MAP1LC3B in complex with Z183352334
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 / autophagy of mitochondrion / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs / cellular response to nitrogen starvation / Receptor Mediated Mitophagy / Macroautophagy / organelle membrane ...SARS-CoV-2 modulates autophagy / ceramide binding / phosphatidylethanolamine binding / autophagy of mitochondrion / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs / cellular response to nitrogen starvation / Receptor Mediated Mitophagy / Macroautophagy / organelle membrane / axoneme / autophagosome membrane / 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 / microtubule binding / cytoplasmic vesicle / 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
: / Microtubule-associated proteins 1A/1B light chain 3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.84 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)14,98411
Polymers14,2371
Non-polymers74610
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.798, 60.798, 35.378
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-K96 / N-{[(2R)-oxolan-2-yl]methyl}morpholine-4-carboxamide


Mass: 214.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H18N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / 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.: 91 / 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: 2.21 Å3/Da / Density % sol: 44.33 % / 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: 1.84→42.98 Å / Num. obs: 11438 / % possible obs: 100 % / Redundancy: 13.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.025 / Rrim(I) all: 0.091 / Net I/σ(I): 13.4 / Num. measured all: 156378 / 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
1.84-1.8814.25.55498126890.2661.5265.7610.399.7
9.01-42.9810.40.03711671120.9990.0120.03970.799.2

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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: 1.84→43.03 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.951 / SU B: 7.135 / SU ML: 0.189 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2454 468 4.2 %RANDOM
Rwork0.1938 ---
obs0.1959 10740 98.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 145.42 Å2 / Biso mean: 53.317 Å2 / Biso min: 29.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å2-0 Å2
2---0.52 Å2-0 Å2
3---1.03 Å2
Refinement stepCycle: final / Resolution: 1.84→43.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms954 0 48 91 1093
Biso mean--78.74 64.74 -
Num. residues----113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0141357
X-RAY DIFFRACTIONr_bond_other_d0.0010.0141237
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.6781656
X-RAY DIFFRACTIONr_angle_other_deg1.2181.5832818
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.515156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.13818.91974
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.54315224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0261515
X-RAY DIFFRACTIONr_chiral_restr0.0760.2154
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021417
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02305
X-RAY DIFFRACTIONr_mcbond_it4.6015.074623
X-RAY DIFFRACTIONr_mcbond_other4.5975.068619
X-RAY DIFFRACTIONr_mcangle_it6.3197.599740
LS refinement shellResolution: 1.84→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 45 -
Rwork0.443 609 -
all-654 -
obs--79.56 %

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