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- PDB-1kko: CRYSTAL STRUCTURE OF CITROBACTER AMALONATICUS METHYLASPARTATE AMM... -

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Basic information

Entry
Database: PDB / ID: 1kko
TitleCRYSTAL STRUCTURE OF CITROBACTER AMALONATICUS METHYLASPARTATE AMMONIA LYASE
Components3-METHYLASPARTATE AMMONIA-LYASE
KeywordsLYASE / Methylaspartate ammonia lyase / Enolase superfamily / Tim barrel
Function / homology
Function and homology information


methylaspartate ammonia-lyase / methylaspartate ammonia-lyase activity / glutamate catabolic process via L-citramalate / metal ion binding
Similarity search - Function
Methylaspartate ammonia-lyase / Methylaspartate ammonia-lyase, C-terminal / Methylaspartate ammonia-lyase, N-terminal / Methylaspartate ammonia-lyase N-terminus / Methylaspartate ammonia-lyase C-terminus / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 ...Methylaspartate ammonia-lyase / Methylaspartate ammonia-lyase, C-terminal / Methylaspartate ammonia-lyase, N-terminal / Methylaspartate ammonia-lyase N-terminus / Methylaspartate ammonia-lyase C-terminus / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Methylaspartate ammonia-lyase
Similarity search - Component
Biological speciesCitrobacter amalonaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsLevy, C.W. / Buckley, P.A. / Sedelnikova, S. / Kato, Y. / Asano, Y. / Rice, D.W. / Baker, P.J.
CitationJournal: Structure / Year: 2002
Title: Insights into enzyme evolution revealed by the structure of methylaspartate ammonia lyase.
Authors: Levy, C.W. / Buckley, P.A. / Sedelnikova, S. / Kato, Y. / Asano, Y. / Rice, D.W. / Baker, P.J.
History
DepositionDec 10, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-METHYLASPARTATE AMMONIA-LYASE
B: 3-METHYLASPARTATE AMMONIA-LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0763
Polymers91,9802
Non-polymers961
Water39,6872203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-43 kcal/mol
Surface area27550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.339, 237.362, 65.806
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-3194-

HOH

21B-456-

HOH

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Components

#1: Protein 3-METHYLASPARTATE AMMONIA-LYASE


Mass: 45989.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter amalonaticus (bacteria) / Gene: MAL / Plasmid: PMAL / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 / References: UniProt: O66145, methylaspartate ammonia-lyase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2203 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: potassium phosphate, ammonium sulphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Details: Levy, C.W., (2001) Acta Crystallogr., D57, 1922.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
113 mg/mlprotein1drop
20.1 Mpotassium phosphate1reservoirpH8.0
332 %ammonium sulfate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97963,0.97946,0.96863
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEOct 30, 1999
ADSC QUANTUM 42CCDOct 30, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979631
20.979461
30.968631
ReflectionResolution: 1.3→119 Å / Num. all: 245233 / Num. obs: 245233 / Redundancy: 3.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.9
Reflection shellResolution: 1.33→1.36 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 3.5 / % possible all: 97.2
Reflection
*PLUS
Highest resolution: 1.33 Å / Lowest resolution: 20 Å / % possible obs: 95.8 % / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 97.2 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
REFMACrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→119.52 Å / SU B: 1.849 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.05
RfactorNum. reflection% reflectionSelection details
Rfree0.19083 11797 5 %RANDOM
Rwork0.161 ---
obs0.162 222972 95.73 %-
Displacement parametersBiso mean: 14.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.33→119.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6322 0 5 2203 8530
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_mcbond_it0.0110.798
X-RAY DIFFRACTIONp_mcangle_it1.41.308
X-RAY DIFFRACTIONp_scbond_it1.916
X-RAY DIFFRACTIONp_scangle_it2.913
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.174 / Rfactor Rfree: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.4
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it

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