[English] 日本語
Yorodumi- PDB-5zyr: Crystal structure of the reductase (C1) component of p-hydroxyphe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zyr | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the reductase (C1) component of p-hydroxyphenylacetate 3-hydroxylase (HPAH) from Acinetobacter baumannii | |||||||||
Components | p-hydroxyphenylacetate 3-hydroxylase, reductase component | |||||||||
Keywords | FLAVOPROTEIN / Reductase / Monooxygenase / Acinetobacter baumannii | |||||||||
Function / homology | Function and homology information flavin reductase (NADH) / flavin reductase (NADH) activity / riboflavin reductase (NADPH) activity / : / FMN binding Similarity search - Function | |||||||||
Biological species | Acinetobacter baumannii (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.20001320062 Å | |||||||||
Authors | Oonanant, W. / Phongsak, T. / Sucharitakul, J. / Chaiyen, P. / Yuvaniyama, J. | |||||||||
Funding support | Thailand, 2items
| |||||||||
Citation | Journal: To Be Published Title: Crystal structure of the reductase (C1) component of p-hydroxyphenylacetate 3-hydroxylase (HPAH) from Acinetobacter baumannii Authors: Oonanant, W. / Phongsak, T. / Sucharitakul, J. / Chaiyen, P. / Yuvaniyama, J. #1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. Year: 2012 Title: Crystallization and preliminary X-ray analysis of the reductase component of p-hydroxyphenylacetate 3-hydroxylase from Acinetobacter baumannii Authors: Oonanant, W. / Sucharitakul, J. / Chaiyen, P. / Yuvaniyama, J. #2: Journal: J. Biol. Chem. / Year: 2012 Title: The C-terminal domain of 4-hydroxyphenylacetate 3-hydroxylase from Acinetobacter baumannii is an autoinhibitory domain Authors: Phongsak, T. / Sucharitakul, J. / Thotsaporn, K. / Oonanant, W. / Yuvaniyama, J. / Svasti, J. / Ballou, D.P. / Chaiyen, P. #3: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010 Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution. Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart / Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5zyr.cif.gz | 312.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5zyr.ent.gz | 212 KB | Display | PDB format |
PDBx/mmJSON format | 5zyr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zyr_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5zyr_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5zyr_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | 5zyr_validation.cif.gz | 34.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zy/5zyr ftp://data.pdbj.org/pub/pdb/validation_reports/zy/5zyr | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Experimental dataset #1 | Data reference: 10.1107/S1744309112016909 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 35455.227 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: C1-hpah / Production host: Escherichia coli (E. coli) / References: UniProt: Q6Q271, flavin reductase (NADH) #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.42 % / Description: Yellow rod shape with a tapered end |
---|---|
Crystal grow | Temperature: 295 K / Method: microbatch / pH: 4.6 / Details: PEG 400, sodium acetate, glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 25, 2007 |
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→50 Å / Num. obs: 31616 / % possible obs: 97.2 % / Redundancy: 4.9 % / Biso Wilson estimate: 42.81 Å2 / Rmerge(I) obs: 0.119 / Χ2: 0.981 / Net I/σ(I): 9.45 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 1.83 / Num. unique obs: 2591 / Χ2: 0.768 / % possible all: 81.2 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.20001320062→29.9528 Å / SU ML: 0.273500794138 / Cross valid method: FREE R-VALUE / σ(F): 1.33649246174 / Phase error: 23.0556794462 Details: Atoms with zero occupancy have unobserved density and are modeled with the most probable rotamer that does not clash with other surrounding atoms.
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.3670044805 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.20001320062→29.9528 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|