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Yorodumi- PDB-8khm: Crystal structure of human methionine aminopeptidase 12 (MAP12) i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8khm | ||||||||||||||||||
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Title | Crystal structure of human methionine aminopeptidase 12 (MAP12) in the unbound form | ||||||||||||||||||
Components | Methionine aminopeptidase 1D, mitochondrial | ||||||||||||||||||
Keywords | HYDROLASE / Methionine aminopeptidase / Metal-activated proteases / Mitochondrial-targeted protein | ||||||||||||||||||
Function / homology | Function and homology information N-terminal protein amino acid modification / peptidyl-methionine modification / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / metalloexopeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / mitochondrion / proteolysis / metal ion binding Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å | ||||||||||||||||||
Authors | Lee, Y. / Lee, E. / Hahn, H. / Kim, H. / Heo, Y. / Jang, D.M. / Kim, H.J. / Kim, H.S. | ||||||||||||||||||
Funding support | Korea, Republic Of, 5items
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Citation | Journal: Sci Rep / Year: 2023 Title: Structural insights into N-terminal methionine cleavage by the human mitochondrial methionine aminopeptidase, MetAP1D. Authors: Lee, Y. / Kim, H. / Lee, E. / Hahn, H. / Heo, Y. / Jang, D.M. / Kwak, K. / Kim, H.J. / Kim, H.S. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8khm.cif.gz | 79 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8khm.ent.gz | 55.8 KB | Display | PDB format |
PDBx/mmJSON format | 8khm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kh/8khm ftp://data.pdbj.org/pub/pdb/validation_reports/kh/8khm | HTTPS FTP |
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-Related structure data
Related structure data | 8khnC 8khoC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34384.621 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: METAP1D, MAP1D / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6UB28, methionyl aminopeptidase | ||||
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#2: Chemical | ChemComp-PGE / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 43.65 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop Details: 0.1M HEPES pH 7.2, 0.1M Carboxylic acids, 17% (v/v) MPD, 17% (w/v) PEG 1000, 17% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97957 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 17, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97957 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.39→27.67 Å / Num. obs: 58324 / % possible obs: 99.3 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.073 / Net I/σ(I): 12.83 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.39→27.67 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.39→27.67 Å
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Refine LS restraints |
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LS refinement shell |
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