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- PDB-3zvh: Methylaspartate ammonia lyase from Clostridium tetanomorphum muta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3zvh | ||||||
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Title | Methylaspartate ammonia lyase from Clostridium tetanomorphum mutant Q73A | ||||||
![]() | (METHYLASPARTATE AMMONIA- ...) x 2 | ||||||
![]() | LYASE / ENOLASE | ||||||
Function / homology | ![]() methylaspartate ammonia-lyase / methylaspartate ammonia-lyase activity / glutamate catabolic process via L-citramalate / cobalamin binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Raj, H. / Szymanski, W. / de Villiers, J. / Rozeboom, H.J. / Veetil, V.P. / Reis, C.R. / de Villiers, M. / de Wildeman, S. / Dekker, F.J. / Quax, W.J. ...Raj, H. / Szymanski, W. / de Villiers, J. / Rozeboom, H.J. / Veetil, V.P. / Reis, C.R. / de Villiers, M. / de Wildeman, S. / Dekker, F.J. / Quax, W.J. / Thunnissen, A.M.W.H. / Feringa, B.L. / Janssen, D.B. / Poelarends, G.J. | ||||||
![]() | ![]() Title: Engineering Methylaspartate Ammonia Lyase for the Asymmetric Synthesis of Unnatural Amino Acids. Authors: Raj, H. / Szymanski, W. / De Villiers, J. / Rozeboom, H.J. / Veetil, V.P. / Reis, C.R. / De Villiers, M. / Dekker, F.J. / De Wildeman, S. / Quax, W.J. / Thunnissen, A.M.W.H. / Feringa, B.L. ...Authors: Raj, H. / Szymanski, W. / De Villiers, J. / Rozeboom, H.J. / Veetil, V.P. / Reis, C.R. / De Villiers, M. / Dekker, F.J. / De Wildeman, S. / Quax, W.J. / Thunnissen, A.M.W.H. / Feringa, B.L. / Janssen, D.B. / Poelarends, G.J. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 328.3 KB | Display | ![]() |
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PDB format | ![]() | 266 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.6 KB | Display | ![]() |
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Full document | ![]() | 468.9 KB | Display | |
Data in XML | ![]() | 36.1 KB | Display | |
Data in CIF | ![]() | 53 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3zviC ![]() 1kczS 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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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-1, 0.004411, -0.006059), Vector: |
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Components
-METHYLASPARTATE AMMONIA- ... , 2 types, 2 molecules AB
#1: Protein | Mass: 48449.262 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 48481.262 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 4 types, 540 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE |
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Crystal grow | pH: 6 / Details: 14-17 % PEG6000, MES PH 6.0, 100 MM MGCL2 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Nov 10, 2010 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→38.9 Å / Num. obs: 54091 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.1 / % possible all: 95.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1KCZ Resolution: 1.99→77.71 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.875 / SU B: 7.887 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 14.506 Å2
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Refinement step | Cycle: LAST / Resolution: 1.99→77.71 Å
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Refine LS restraints |
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