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Yorodumi- PDB-1mmt: Crystal structure of ternary complex of the catalytic domain of h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mmt | ||||||
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Title | Crystal structure of ternary complex of the catalytic domain of human phenylalanine hydroxylase (Fe(II)) complexed with tetrahydrobiopterin and norleucine | ||||||
Components | Phenylalanine-4-hydroxylase | ||||||
Keywords | OXIDOREDUCTASE / BASKET-ARRANGEMENT / 13 ALPHA-HELICES / 8 BETA-STRANDS / FERROUS IRON | ||||||
Function / homology | Function and homology information Phenylketonuria / Phenylalanine metabolism / phenylalanine 4-monooxygenase / phenylalanine 4-monooxygenase activity / tyrosine biosynthetic process / catecholamine biosynthetic process / L-phenylalanine catabolic process / amino acid biosynthetic process / iron ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / phases adopted from 1KW0 / Resolution: 2 Å | ||||||
Authors | Andersen, O.A. / Flatmark, T. / Hough, E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: 2.0A resolution crystal structures of the ternary complexes of human phenylalanine hydroxylase catalytic domain with tetrahydrobiopterin and 3-(2-thienyl)-L-alanine or L-norleucine: substrate ...Title: 2.0A resolution crystal structures of the ternary complexes of human phenylalanine hydroxylase catalytic domain with tetrahydrobiopterin and 3-(2-thienyl)-L-alanine or L-norleucine: substrate specificity and molecular motions related to substrate binding Authors: Andersen, O.A. / Stokka, A.J. / Flatmark, T. / Hough, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mmt.cif.gz | 81.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mmt.ent.gz | 58.9 KB | Display | PDB format |
PDBx/mmJSON format | 1mmt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mmt_validation.pdf.gz | 459.5 KB | Display | wwPDB validaton report |
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Full document | 1mmt_full_validation.pdf.gz | 462.3 KB | Display | |
Data in XML | 1mmt_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 1mmt_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mm/1mmt ftp://data.pdbj.org/pub/pdb/validation_reports/mm/1mmt | HTTPS FTP |
-Related structure data
Related structure data | 1mmkC 1kw0S 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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Details | THE SECOND PART OF THE BIOLOGICAL DIMER IS GENERATED BY: -x, y, 1/2-z |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37601.570 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN (RESIDUES 103-427) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PAH / Plasmid: PMAL / Production host: Escherichia coli (E. coli) / References: UniProt: P00439, phenylalanine 4-monooxygenase |
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-Non-polymers , 5 types, 153 molecules
#2: Chemical | ChemComp-FE2 / |
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#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-H4B / |
#5: Chemical | ChemComp-NLE / |
#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: 2.85 Å3/Da / Density % sol: 56.89 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 20% PEG 2000, 12% ethylene glycol, 0.12M Na-Hepes, 10mM BH4, 30mM Na-dithionite, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.8 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 2, 2002 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 28552 / Num. obs: 28552 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 2.2 / Num. unique all: 4197 / Rsym value: 0.275 / % possible all: 99.1 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 99.1 % / Num. unique obs: 4197 |
-Processing
Software |
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Refinement | Method to determine structure: phases adopted from 1KW0 Starting model: PDB ENTRY 1KW0 Resolution: 2→10 Å / Isotropic thermal model: overall anisotropic b value / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 28.7 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.01 Å /
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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