[English] 日本語
Yorodumi- PDB-8jqp: Protocatecuate hydroxylase from Xylophilus ampelinus complexed wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8jqp | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Protocatecuate hydroxylase from Xylophilus ampelinus complexed with 3,4-dihydroxybenzoate | |||||||||
Components | 4-hydroxybenzoate 3-monooxygenase (NAD(P)H) | |||||||||
Keywords | OXIDOREDUCTASE / p-hydroxybenzoate hydroxylase / FAD / NADPH | |||||||||
Function / homology | 3,4-DIHYDROXYBENZOIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / : Function and homology information | |||||||||
Biological species | Xylophilus ampelinus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | |||||||||
Authors | Fukushima, R. / Katsuki, N. / Fushinobu, S. / Takaya, N. | |||||||||
Funding support | Japan, 2items
| |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2023 Title: Protocatechuate hydroxylase is a novel group A flavoprotein monooxygenase with a unique substrate recognition mechanism. Authors: Katsuki, N. / Fukushima, R. / Doi, Y. / Masuo, S. / Arakawa, T. / Yamada, C. / Fushinobu, S. / Takaya, N. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8jqp.cif.gz | 223.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8jqp.ent.gz | 140.3 KB | Display | PDB format |
PDBx/mmJSON format | 8jqp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jqp_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8jqp_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 8jqp_validation.xml.gz | 34.2 KB | Display | |
Data in CIF | 8jqp_validation.cif.gz | 52 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/8jqp ftp://data.pdbj.org/pub/pdb/validation_reports/jq/8jqp | HTTPS FTP |
-Related structure data
Related structure data | 8jqoC 8jqqC 1k0iS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 45531.746 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xylophilus ampelinus (bacteria) / Gene: praI / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: A0A978C2P2 |
---|
-Non-polymers , 5 types, 611 molecules
#2: Chemical | #3: Chemical | ChemComp-DHB / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.8 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 6% PEG 8000, 0.24 M Calcium acetate, 0.1 M Tris, Soaked with 20 mM 3,4-dihydroxybenzoate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 24, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→47.52 Å / Num. obs: 86275 / % possible obs: 100 % / Redundancy: 3.4 % / Biso Wilson estimate: 18.65 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.031 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4251 / CC1/2: 0.816 / Rpim(I) all: 0.319 / % possible all: 99.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1K0I Resolution: 1.65→47.52 Å / SU ML: 0.2086 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 21.4253 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.91 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→47.52 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|