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- PDB-2bp7: New crystal form of the Pseudomonas putida branched-chain dehydro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2bp7 | ||||||
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Title | New crystal form of the Pseudomonas putida branched-chain dehydrogenase (E1) | ||||||
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![]() | OXIDOREDUCTASE / FLAVOPROTEIN / THDP COFACTOR | ||||||
Function / homology | ![]() 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) / 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Frank, R.A.W. / Pratap, J.V. / Pei, X.Y. / Perham, R.N. / Luisi, B.F. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 556.7 KB | Display | ![]() |
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PDB format | ![]() | 461.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 487.2 KB | Display | ![]() |
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Full document | ![]() | 537.5 KB | Display | |
Data in XML | ![]() | 100.9 KB | Display | |
Data in CIF | ![]() | 137.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qs0S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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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: |
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Components
#1: Protein | Mass: 45318.996 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() 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.) ![]() ![]() ![]() References: UniProt: P09061, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 63 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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.
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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: 35.72 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→20 Å
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Refine LS restraints |
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