+Open data
-Basic information
Entry | Database: PDB / ID: 7oeq | ||||||
---|---|---|---|---|---|---|---|
Title | Mevalonyl-coenzyme A hydratase (Sid H) | ||||||
Components | Mevalonyl-coenzyme A hydratase sidH | ||||||
Keywords | LYASE / hydratase | ||||||
Function / homology | Function and homology information N',N'',N'''-triacetylfusarinine C biosynthetic process / cellular response to iron ion starvation / Lyases; Carbon-oxygen lyases; Hydro-lyases / ergosterol biosynthetic process / isomerase activity / cellular response to hydrogen peroxide / peroxisome / lyase activity Similarity search - Function | ||||||
Biological species | Neosartorya fumigata (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.36 Å | ||||||
Authors | Poonsiri, T. / Demitri, N. / Benini, S. | ||||||
Funding support | Italy, 1items
| ||||||
Citation | Journal: To Be Published Title: Mevalonyl-coenzyme A hydratase (Sid H) Authors: Poonsiri, T. / Demitri, N. / Benini, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7oeq.cif.gz | 120.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7oeq.ent.gz | 93.5 KB | Display | PDB format |
PDBx/mmJSON format | 7oeq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7oeq_validation.pdf.gz | 395.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7oeq_full_validation.pdf.gz | 395.3 KB | Display | |
Data in XML | 7oeq_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | 7oeq_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/7oeq ftp://data.pdbj.org/pub/pdb/validation_reports/oe/7oeq | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 29375.564 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold) Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: sidH, AFUA_3G03410 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): B References: UniProt: Q4WF54, Lyases; Carbon-oxygen lyases; Hydro-lyases |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.23 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.22 M Sodium formate, 0.1 M Bis-Tris propane pH 6.5, 17 % w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2021 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.36→46.58 Å / Num. obs: 69076 / % possible obs: 99.9 % / Redundancy: 6.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.038 / Rrim(I) all: 0.096 / Net I/σ(I): 8.6 / Num. measured all: 423091 / Scaling rejects: 373 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: MrBUMP 3kqf_F1_SCLPTR Resolution: 1.36→42.93 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.972 / SU B: 2.943 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.045 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 max: 88.01 Å2 / Biso mean: 22.38 Å2 / Biso min: 12.8 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.36→42.93 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.36→1.395 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|