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Yorodumi- PDB-6ecr: The human methylenetetrahydrofolate dehydrogenase/cyclohydrolase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ecr | ||||||
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Title | The human methylenetetrahydrofolate dehydrogenase/cyclohydrolase (FolD) complexed with NADP | ||||||
Components | methylenetetrahydrofolate dehydrogenase cyclohydrolase | ||||||
Keywords | OXIDOREDUCTASE / dehydrogenase / cyclohydrolase / bifunctional protein | ||||||
Function / homology | Function and homology information methylenetetrahydrofolate dehydrogenase [NAD(P)+] activity / serine family amino acid biosynthetic process / 10-formyltetrahydrofolate biosynthetic process / purine ribonucleotide biosynthetic process / serine family amino acid metabolic process / methylenetetrahydrofolate dehydrogenase (NAD+) activity / formate-tetrahydrofolate ligase / formate-tetrahydrofolate ligase activity / methylenetetrahydrofolate dehydrogenase (NADP+) / embryonic neurocranium morphogenesis ...methylenetetrahydrofolate dehydrogenase [NAD(P)+] activity / serine family amino acid biosynthetic process / 10-formyltetrahydrofolate biosynthetic process / purine ribonucleotide biosynthetic process / serine family amino acid metabolic process / methylenetetrahydrofolate dehydrogenase (NAD+) activity / formate-tetrahydrofolate ligase / formate-tetrahydrofolate ligase activity / methylenetetrahydrofolate dehydrogenase (NADP+) / embryonic neurocranium morphogenesis / methenyltetrahydrofolate cyclohydrolase / methenyltetrahydrofolate cyclohydrolase activity / embryonic viscerocranium morphogenesis / methylenetetrahydrofolate dehydrogenase (NADP+) activity / methionine metabolic process / somite development / methionine biosynthetic process / Metabolism of folate and pterines / transsulfuration / neutrophil homeostasis / purine nucleotide biosynthetic process / tetrahydrofolate interconversion / neural tube closure / one-carbon metabolic process / heart development / mitochondrion / extracellular exosome / ATP binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å | ||||||
Authors | Bueno, R.V. / Dawson, A. / Hunter, W.N. | ||||||
Funding support | Brazil, 1items
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Citation | Journal: Biochemistry / Year: 2000 Title: Structures of three inhibitor complexes provide insight into the reaction mechanism of the human methylenetetrahydrofolate dehydrogenase/cyclohydrolase. Authors: Schmidt, A. / Wu, H. / MacKenzie, R.E. / Chen, V.J. / Bewly, J.R. / Ray, J.E. / Toth, J.E. / Cygler, M. | ||||||
History |
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Remark 0 | THIS ENTRY 6ECR REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 1DIG, DETERMINED BY A. ...THIS ENTRY 6ECR REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 1DIG, DETERMINED BY A.Schmidt,H.Wu,R.E.MacKenzie,V.J.Chen,J.R.Bewly,J.E.Ray,J.E.Toth,M.Cygler |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ecr.cif.gz | 130.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ecr.ent.gz | 99.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ecr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ec/6ecr ftp://data.pdbj.org/pub/pdb/validation_reports/ec/6ecr | HTTPS FTP |
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-Related structure data
Related structure data | 6ecpC 6ecqC 1digS S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 0 / Auth seq-ID: 2 - 296 / Label seq-ID: 2 - 296
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-Components
#1: Protein | Mass: 32090.848 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MTHFD1, MTHFC, MTHFD / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P11586, methylenetetrahydrofolate dehydrogenase (NADP+), methenyltetrahydrofolate cyclohydrolase, formate-tetrahydrofolate ligase #2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Water | ChemComp-HOH / | |
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-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: 44.63 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 1DIG |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: PEG 3350, GLYCEROL, SODIUM CITRATE, AMMONIUM ACETATE, pH 5.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 20K. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 30, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→15 Å / Num. obs: 29810 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.2→2.23 Å / Redundancy: 5 % / Rmerge(I) obs: 0.147 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1DIG Resolution: 2.2→14.92 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.162 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.316 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.67 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→14.92 Å
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Refine LS restraints |
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