+Open data
-Basic information
Entry | Database: PDB / ID: 4wmx | |||||||||
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Title | The structure of MBP-MCL1 bound to ligand 6 at 2.0A | |||||||||
Components | MBP-MCL1 chimera protein | |||||||||
Keywords | APOPTOSIS / protein-protein interaction | |||||||||
Function / homology | Function and homology information positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cell fate determination / cellular homeostasis / channel activity / mitochondrial fusion / Bcl-2 family protein complex / BH domain binding / detection of maltose stimulus / maltose transport complex / BH3 domain binding ...positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cell fate determination / cellular homeostasis / channel activity / mitochondrial fusion / Bcl-2 family protein complex / BH domain binding / detection of maltose stimulus / maltose transport complex / BH3 domain binding / carbohydrate transport / negative regulation of anoikis / carbohydrate transmembrane transporter activity / protein transmembrane transporter activity / maltose binding / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / extrinsic apoptotic signaling pathway in absence of ligand / ATP-binding cassette (ABC) transporter complex / negative regulation of autophagy / cell chemotaxis / release of cytochrome c from mitochondria / response to cytokine / intrinsic apoptotic signaling pathway in response to DNA damage / Signaling by ALK fusions and activated point mutants / outer membrane-bounded periplasmic space / Interleukin-4 and Interleukin-13 signaling / regulation of apoptotic process / mitochondrial outer membrane / periplasmic space / protein heterodimerization activity / positive regulation of apoptotic process / DNA damage response / negative regulation of apoptotic process / mitochondrion / nucleoplasm / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Clifton, M.C. / Dranow, D.M. | |||||||||
Citation | Journal: Plos One / Year: 2015 Title: A Maltose-Binding Protein Fusion Construct Yields a Robust Crystallography Platform for MCL1. Authors: Clifton, M.C. / Dranow, D.M. / Leed, A. / Fulroth, B. / Fairman, J.W. / Abendroth, J. / Atkins, K.A. / Wallace, E. / Fan, D. / Xu, G. / Ni, Z.J. / Daniels, D. / Van Drie, J. / Wei, G. / ...Authors: Clifton, M.C. / Dranow, D.M. / Leed, A. / Fulroth, B. / Fairman, J.W. / Abendroth, J. / Atkins, K.A. / Wallace, E. / Fan, D. / Xu, G. / Ni, Z.J. / Daniels, D. / Van Drie, J. / Wei, G. / Burgin, A.B. / Golub, T.R. / Hubbard, B.K. / Serrano-Wu, M.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wmx.cif.gz | 223.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wmx.ent.gz | 173.7 KB | Display | PDB format |
PDBx/mmJSON format | 4wmx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wmx_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 4wmx_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4wmx_validation.xml.gz | 22.9 KB | Display | |
Data in CIF | 4wmx_validation.cif.gz | 34.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/4wmx ftp://data.pdbj.org/pub/pdb/validation_reports/wm/4wmx | HTTPS FTP |
-Related structure data
Related structure data | 4wmrC 4wmsC 4wmtC 4wmuC 4wmvC 4wmwC 4mbpS 4oq6S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 57310.883 Da / Num. of mol.: 1 Fragment: UNP P0AEX9 residues 27-392,UNP Q07820 residues 174-321 Mutation: K194A, K197A, R201A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human) Strain: K12 / Gene: malE, b4034, JW3994, MCL1, BCL2L3 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: Q07820 |
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
-Non-polymers , 4 types, 379 molecules
#3: Chemical | ChemComp-3R7 / | ||||
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#4: Chemical | ChemComp-FMT / #5: Chemical | ChemComp-MG / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.48 % / Description: Rods |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 10 MG/ML MBP-MCL1, 200MM MG FORMATE, 20% PEG3350, 1MM MALTOSE, 2MM ligand 6, CRYOPROTECTANT 20% ETHYLENE GLYCOL, PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 15, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. obs: 34824 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Biso Wilson estimate: 23 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.09 / Χ2: 0.881 / Net I/σ(I): 20.58 / Num. measured all: 297756 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OQ6,4MBP Resolution: 2→46.327 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.6 Å2 / Biso mean: 26.1347 Å2 / Biso min: 11.81 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→46.327 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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