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- PDB-2zy2: dodecameric L-aspartate beta-decarboxylase -

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Basic information

Entry
Database: PDB / ID: 2zy2
Titledodecameric L-aspartate beta-decarboxylase
ComponentsL-aspartate 4-carboxylyase
KeywordsLYASE / pyridoxal 5'-phosphate / aminotransferase
Function / homology
Function and homology information


aspartate 4-decarboxylase / aspartate 4-decarboxylase activity / alanine biosynthetic process / aspartate metabolic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / pyridoxal phosphate binding / identical protein binding
Similarity search - Function
Histone, subunit A - #110 / Aspartate 4-decarboxylase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Histone, subunit A / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Pyridoxal phosphate-dependent transferase, small domain ...Histone, subunit A - #110 / Aspartate 4-decarboxylase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Histone, subunit A / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Bifunctional aspartate aminotransferase and L-aspartate beta-decarboxylase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.3 Å
AuthorsChen, H.-J. / Ko, T.-P. / Lee, C.-Y. / Wang, N.-C. / Wang, A.H.-J.
CitationJournal: Structure / Year: 2009
Title: Structure, Assembly, and Mechanism of a PLP-Dependent Dodecameric l-Aspartate beta-Decarboxylase
Authors: Chen, H.-J. / Ko, T.-P. / Lee, C.-Y. / Wang, N.-C. / Wang, A.H.-J.
History
DepositionJan 13, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-aspartate 4-carboxylyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0862
Polymers60,8391
Non-polymers2471
Water66737
1
A: L-aspartate 4-carboxylyase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)733,03724
Polymers730,07112
Non-polymers2,96612
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation28_555x,-y+1/2,-z+1/21
crystal symmetry operation30_555z,-x+1/2,-y+1/21
crystal symmetry operation35_555y,-z+1/2,-x+1/21
crystal symmetry operation51_555-x+1/2,y,-z+1/21
crystal symmetry operation56_555-z+1/2,x,-y+1/21
crystal symmetry operation58_555-y+1/2,z,-x+1/21
crystal symmetry operation74_555-x+1/2,-y+1/2,z1
crystal symmetry operation79_555-z+1/2,-x+1/2,y1
crystal symmetry operation84_555-y+1/2,-z+1/2,x1
Buried area80340 Å2
ΔGint-242 kcal/mol
Surface area206850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)298.900, 298.900, 298.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-704-

HOH

21A-705-

HOH

31A-716-

HOH

41A-729-

HOH

51A-730-

HOH

61A-743-

HOH

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Components

#1: Protein L-aspartate 4-carboxylyase


Mass: 60839.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: ATCC 19121 / Gene: asdP / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q53IZ1, aspartate 4-decarboxylase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 1

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Sample preparation

CrystalDensity Matthews: 4.57 Å3/Da / Density % sol: 73.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 40% PEG 400, 0.1M lithium sulfate, 0.1M Tris-HCl (pH 8.5), VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSRRC BL13B111
SYNCHROTRONNSRRC BL13B120.991, 1.010
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDNov 2, 2006Vertically Collimating Premirror, Toroidal Focusing Mirror
ADSC QUANTUM 3152CCDMay 22, 2007
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LN2-Cooled Fixed-Exit Double Crystal Si(111) MonochromatorSINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.9911
31.011
ReflectionResolution: 3.3→30 Å / Num. all: 17736 / Num. obs: 17608 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 10.8 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 23.4
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1706 / % possible all: 98.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 3.3→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Initial phasing by HgCl2 derivative data collected at two wavelengths 0.991 and 1.010 Angstroms to 4.75 Angstroms resolution
RfactorNum. reflection% reflectionSelection details
Rfree0.293 767 -RANDOM
Rwork0.228 ---
all0.231 17736 --
obs0.231 16032 90.4 %-
Solvent computationBsol: 26.849 Å2
Displacement parametersBiso max: 164.43 Å2 / Biso mean: 77.655 Å2 / Biso min: 21.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 3.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4095 0 15 37 4147
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.87551
X-RAY DIFFRACTIONc_bond_d0.014641
LS refinement shellResolution: 3.3→3.42 Å / Rfactor Rfree error: 0.0164
RfactorNum. reflection% reflection
Rfree0.2984 57 -
Rwork0.282 --
obs-1403 81.8 %

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