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- PDB-2xed: Nocardia farcinica maleate cis-trans isomerase C194S mutant with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xed | ||||||
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Title | Nocardia farcinica maleate cis-trans isomerase C194S mutant with a covalently bound succinylcysteine intermediate | ||||||
![]() | PUTATIVE MALEATE ISOMERASE![]() | ||||||
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Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fisch, F. / Martinez-Fleites, C. / Baudendistel, N. / Hauer, B. / Turkenburg, J.P. / Hart, S. / Bruce, N.C. / Grogan, G. | ||||||
![]() | ![]() Title: A Covalent Succinylcysteine-Like Intermediate in the Enzyme-Catalyzed Transformation of Maleate to Fumarate by Maleate Isomerase. Authors: Fisch, F. / Fleites, C.M. / Delenne, M. / Baudendistel, N. / Hauer, B. / Turkenburg, J.P. / Hart, S. / Bruce, N.C. / Grogan, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 382.8 KB | Display | ![]() |
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PDB format | ![]() | 315.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2xecSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 28826.975 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Details: COVALENT LINK BETWEEN CYS76 AND SUCCINYL LIKE INTERMEDIATE Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SIN / ![]() #3: Water | ChemComp-HOH / | ![]() Compound details | ENGINEERED RESIDUE IN CHAIN A, CYS 194 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS 194 TO ALA ...ENGINEERED | Nonpolymer details | SUCCINYL-LIKE COVALENT INTERMEDIA | Sequence details | C194A | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE |
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Crystal grow![]() | pH: 6.5 Details: 20 MM NH4 FORMATE 100 MM MES PH 6.5 20% PEG 3350 50 MM NA MALEATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 6, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.95→52.98 Å / Num. obs: 80183 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.3 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2XEC Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.903 / SU B: 9.723 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.907 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→20 Å
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Refine LS restraints |
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