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Yorodumi- PDB-8cp2: Structure of Aspartate-N-hydroxylase (FzmM)from Streptomyces sp. ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cp2 | ||||||
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Title | Structure of Aspartate-N-hydroxylase (FzmM)from Streptomyces sp. V2: complex with NADPH and L-aspartate | ||||||
Components | FAD-binding protein | ||||||
Keywords | OXIDOREDUCTASE / Monooxygenase / flavin / aspartate | ||||||
Function / homology | FAD-dependent urate hydroxylase HpyO, FAD/NAD(P)-binding domain / FAD-NAD(P)-binding / FAD/NAD(P)-binding domain superfamily / 3-NITROPROPANOIC ACID / ASPARTIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / DI(HYDROXYETHYL)ETHER / FAD-binding protein Function and homology information | ||||||
Biological species | Streptomyces sp. V2 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Rotilio, L. / Mattevi, A. | ||||||
Funding support | Italy, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2023 Title: A biosynthetic aspartate N-hydroxylase performs successive oxidations by holding intermediates at a site away from the catalytic center. Authors: Rotilio, L. / Boverio, A. / Nguyen, Q.T. / Mannucci, B. / Fraaije, M.W. / Mattevi, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cp2.cif.gz | 266.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cp2.ent.gz | 211.3 KB | Display | PDB format |
PDBx/mmJSON format | 8cp2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cp2_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 8cp2_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 8cp2_validation.xml.gz | 53 KB | Display | |
Data in CIF | 8cp2_validation.cif.gz | 77.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/8cp2 ftp://data.pdbj.org/pub/pdb/validation_reports/cp/8cp2 | HTTPS FTP |
-Related structure data
Related structure data | 8cp5C 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 65830.266 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. V2 (bacteria) / Gene: DF268_28005 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RP+ / References: UniProt: A0A2V1NMV1 |
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-Non-polymers , 7 types, 811 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-3NP / | #6: Chemical | ChemComp-PEG / #7: Chemical | ChemComp-GOL / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 9% PEG 4000, 1.2 M di-Na tartrate |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 27, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87313 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→122.3 Å / Num. obs: 166781 / % possible obs: 100 % / Redundancy: 10.6 % / CC1/2: 0.993 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.093 / Rrim(I) all: 0.301 / Χ2: 1.03 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.1→2.14 Å / % possible obs: 100 % / Redundancy: 10.9 % / Rmerge(I) obs: 1.8 / Num. measured all: 90751 / Num. unique obs: 8301 / CC1/2: 0.473 / Rpim(I) all: 0.736 / Rrim(I) all: 2.439 / Χ2: 0.99 / Net I/σ(I) obs: 1.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→122.3 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.007 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.11 / 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: 33.891 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→122.3 Å
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