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- PDB-2zy3: dodecameric L-aspartate beta-decarboxylase -

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Basic information

Entry
Database: PDB / ID: 2zy3
Titledodecameric L-aspartate beta-decarboxylase
ComponentsL-aspartate beta-decarboxylase
KeywordsLYASE / pyridoxal 5'-phosphate / aminotransferase
Function / homology
Function and homology information


aspartate 4-decarboxylase / aspartate 4-decarboxylase activity / 1-aminocyclopropane-1-carboxylate synthase 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 speciesAlcaligenes faecalis subsp. faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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: Non-polymer description / Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-aspartate beta-decarboxylase
B: L-aspartate beta-decarboxylase
C: L-aspartate beta-decarboxylase
D: L-aspartate beta-decarboxylase
E: L-aspartate beta-decarboxylase
F: L-aspartate beta-decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)368,52412
Polymers367,0416
Non-polymers1,4836
Water39,5072193
1
A: L-aspartate beta-decarboxylase
B: L-aspartate beta-decarboxylase
C: L-aspartate beta-decarboxylase
D: L-aspartate beta-decarboxylase
E: L-aspartate beta-decarboxylase
F: L-aspartate beta-decarboxylase
hetero molecules

A: L-aspartate beta-decarboxylase
B: L-aspartate beta-decarboxylase
C: L-aspartate beta-decarboxylase
D: L-aspartate beta-decarboxylase
E: L-aspartate beta-decarboxylase
F: L-aspartate beta-decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)737,04724
Polymers734,08212
Non-polymers2,96612
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area79550 Å2
ΔGint-246 kcal/mol
Surface area190590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.734, 216.141, 208.726
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2072-

HOH

21C-1300-

HOH

31C-1807-

HOH

41C-2185-

HOH

51E-1718-

HOH

61E-1721-

HOH

71E-1722-

HOH

81E-1731-

HOH

91E-1824-

HOH

101F-1978-

HOH

111F-1979-

HOH

121F-2207-

HOH

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Components

#1: Protein
L-aspartate beta-decarboxylase


Mass: 61173.480 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes faecalis subsp. faecalis (bacteria)
Strain: subsp. faecalis / Gene: asdA-AF / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q93QX0, aspartate 4-decarboxylase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2193 / 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: 2.3 Å3/Da / Density % sol: 46.53 %
Crystal growTemperature: 277 K / Method: hanging drop / pH: 7.4
Details: 0.1M Tris-HCl (pH 7.4), 0.1M Lithium sulfate, 15% PEG 4000, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL17B2 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 6, 2003 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 116669 / Num. obs: 115036 / % possible obs: 98.6 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 11.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.03 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.4 / Num. unique all: 11108 / % possible all: 96.1

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Processing

Software
NameClassification
Blu-Icedata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZY2

2zy2


Resolution: 2.5→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 5434 -RANDOM
Rwork0.175 ---
all0.178 108127 --
obs0.178 102693 92.8 %-
Solvent computationBsol: 44.429 Å2
Displacement parametersBiso max: 121.29 Å2 / Biso mean: 38.795 Å2 / Biso min: 5.81 Å2
Baniso -1Baniso -2Baniso -3
1--1.369 Å20 Å20 Å2
2--5.764 Å20 Å2
3----4.395 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24316 0 90 2193 26599
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.52799
X-RAY DIFFRACTIONc_bond_d0.01127
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.076
RfactorNum. reflection% reflection
Rfree0.321 462 -
Rwork0.245 --
obs-9659 83.7 %

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