[English] 日本語
Yorodumi- PDB-2bp7: New crystal form of the Pseudomonas putida branched-chain dehydro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bp7 | ||||||
---|---|---|---|---|---|---|---|
Title | New crystal form of the Pseudomonas putida branched-chain dehydrogenase (E1) | ||||||
Components |
| ||||||
Keywords | OXIDOREDUCTASE / FLAVOPROTEIN / THDP COFACTOR | ||||||
Function / homology | Function and homology information 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) / 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity Similarity search - Function | ||||||
Biological species | PSEUDOMONAS PUTIDA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Frank, R.A.W. / Pratap, J.V. / Pei, X.Y. / Perham, R.N. / Luisi, B.F. | ||||||
Citation | Journal: Structure / Year: 2005 Title: The Molecular Origins of Specificity in the Assembly of a Multienzyme Complex. Authors: Frank, R.A.W. / Pratap, J.V. / Pei, X.Y. / Perham, R.N. / Luisi, B.F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2bp7.cif.gz | 556.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2bp7.ent.gz | 461.7 KB | Display | PDB format |
PDBx/mmJSON format | 2bp7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bp7_validation.pdf.gz | 487.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2bp7_full_validation.pdf.gz | 537.5 KB | Display | |
Data in XML | 2bp7_validation.xml.gz | 100.9 KB | Display | |
Data in CIF | 2bp7_validation.cif.gz | 137.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/2bp7 ftp://data.pdbj.org/pub/pdb/validation_reports/bp/2bp7 | HTTPS FTP |
-Related structure data
Related structure data | 1qs0S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 4
NCS ensembles :
NCS oper: (Code: given Matrix: (0.930318, -0.311956, 0.192853), Vector: |
-Components
#1: Protein | Mass: 45318.996 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P09060, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) #2: Protein | Mass: 37172.172 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P09061, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 63 % |
---|---|
Crystal grow | pH: 5.6 Details: PROTEIN SAMPLE (1-5 PHOSPHATE PH6.3, 10MM DTT, 4MM MGCL2, 2MM ALPHA-CHLOROISOCAPROATE, 1MM THIAMINE DIPHOSPHATE., pH 5.60 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Date: Mar 5, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→20 Å / Num. obs: 101157 / % possible obs: 89.6 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.9→3 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.4 / % possible all: 33 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QS0 Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.858 / SU B: 14.934 / SU ML: 0.285 / Cross valid method: THROUGHOUT / ESU R Free: 0.461 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS PSEUODOMONAS PUTIDA BRANCHED-CHAIN DEHYDROGENASE E1 STRUCTURE IS A PACKING MODEL OF A NEW CRYSTAL FORM. THE MODEL WAS OBTAINED BY ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS PSEUODOMONAS PUTIDA BRANCHED-CHAIN DEHYDROGENASE E1 STRUCTURE IS A PACKING MODEL OF A NEW CRYSTAL FORM. THE MODEL WAS OBTAINED BY MOLECULAR REPLACEMENT USING THE COORDINATES OF 1QS0, FOLLOWED BY RIGID BODY AND RESTRAINED REFINEMENT. NO MANUAL FITTING OF THE MODEL WAS PERFORMED.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 35.72 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|