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Yorodumi- PDB-3sle: Crystal Structure of the P107C-MauG/pre-Methylamine Dehydrogenase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sle | ||||||
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Title | Crystal Structure of the P107C-MauG/pre-Methylamine Dehydrogenase Complex | ||||||
Components |
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Keywords | OXIDOREDUCTASE/ELECTRON TRANSPORT / Oxidoreductase / OXIDOREDUCTASE-ELECTRON TRANSPORT complex | ||||||
Function / homology | Function and homology information methylamine dehydrogenase (amicyanin) / methylamine dehydrogenase (amicyanin) activity / methylamine metabolic process / aliphatic amine dehydrogenase activity / amine metabolic process / Oxidoreductases / cytochrome-c peroxidase activity / outer membrane-bounded periplasmic space / periplasmic space / electron transfer activity ...methylamine dehydrogenase (amicyanin) / methylamine dehydrogenase (amicyanin) activity / methylamine metabolic process / aliphatic amine dehydrogenase activity / amine metabolic process / Oxidoreductases / cytochrome-c peroxidase activity / outer membrane-bounded periplasmic space / periplasmic space / electron transfer activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Paracoccus denitrificans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.52 Å | ||||||
Authors | Yukl, E.T. / Wilmot, C.M. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Proline 107 is a major determinant in maintaining the structure of the distal pocket and reactivity of the high-spin heme of MauG. Authors: Feng, M. / Jensen, L.M. / Yukl, E.T. / Wei, X. / Liu, A. / Wilmot, C.M. / Davidson, V.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sle.cif.gz | 683.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sle.ent.gz | 566.9 KB | Display | PDB format |
PDBx/mmJSON format | 3sle.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3sle_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 3sle_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 3sle_validation.xml.gz | 66.2 KB | Display | |
Data in CIF | 3sle_validation.cif.gz | 90.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sl/3sle ftp://data.pdbj.org/pub/pdb/validation_reports/sl/3sle | HTTPS FTP |
-Related structure data
Related structure data | 3sjlC 3svwC 3l4mS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 2
NCS ensembles :
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-Components
-Protein / Antibody / Methylamine dehydrogenase ... , 3 types, 6 molecules ABCEDF
#1: Protein | Mass: 41184.656 Da / Num. of mol.: 2 / Fragment: UNP residues 21-387 / Mutation: P107C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: PD 1222 / Gene: mauG, Pden_4736 / Production host: Paracoccus denitrificans (bacteria) / References: UniProt: Q51658, Oxidoreductases #2: Antibody | Mass: 15025.595 Da / Num. of mol.: 2 / Fragment: UNP residues 58-188 Source method: isolated from a genetically manipulated source Details: Immature Madh (premadh) Was Produced in the Absence of the Maug Gene. Trp57 Is Monohydroxylated At the C7 Position Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: PD 1222 / Gene: mauA / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: P22619, EC: 1.4.99.3 #3: Protein | Mass: 42321.152 Da / Num. of mol.: 2 / Fragment: UNP residues 32-417 Source method: isolated from a genetically manipulated source Details: Immature Madh (premadh) Was Produced in the Absence of the Maug Gene. the Alpha Subunit Has the Wild Type Sequence. Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: PD 1222 / Gene: mauB, pden_4730 / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: A1BB97, EC: 1.4.99.3 |
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-Non-polymers , 5 types, 400 molecules
#4: Chemical | #5: Chemical | ChemComp-HEC / #6: Chemical | ChemComp-ACT / #7: Chemical | #8: 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: 2.38 Å3/Da / Density % sol: 48.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 0.1M MES pH 6.4, 0.1M sodium acetate, 24-30 % w/v PEG 8000, vapor diffusion, hanging drop, temperature 293K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 4, 2010 / Details: BIOMORPH MIRRORS (KIRKPATRICK-BAEZ CONFIGURATION) |
Radiation | Monochromator: Si(111) Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.52→50 Å / Num. all: 61043 / Num. obs: 59309 / % possible obs: 97.16 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 13.85 |
Reflection shell | Resolution: 2.52→2.56 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 3.44 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3L4M Resolution: 2.52→47.86 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.92 / SU B: 25.785 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R: 2.287 / ESU R Free: 0.314 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.772 Å2
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Refinement step | Cycle: LAST / Resolution: 2.52→47.86 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.521→2.586 Å / Total num. of bins used: 20
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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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