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- PDB-2zy5: R487A mutant of L-aspartate beta-decarboxylase -

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Basic information

Entry
Database: PDB / ID: 2zy5
TitleR487A mutant of 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: 2.65 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 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)368,00712
Polymers366,5246
Non-polymers1,4836
Water34,2101899
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)736,01424
Polymers733,04812
Non-polymers2,96612
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area79280 Å2
ΔGint-237 kcal/mol
Surface area188990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.953, 216.215, 208.582
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
11C-1544-

HOH

21E-1477-

HOH

31E-1485-

HOH

41E-1513-

HOH

51E-1559-

HOH

61F-1693-

HOH

71F-1867-

HOH

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Components

#1: Protein
L-aspartate beta-decarboxylase


Mass: 61087.363 Da / Num. of mol.: 6 / Mutation: R487A
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


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


Mass: 18.015 Da / Num. of mol.: 1899 / 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: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 15% PEG 4000, 0.1M lithium sulfate, 0.1M Tris-HCl (pH7.4), VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 28, 2007 / 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: 2.65→30 Å / Num. all: 105354 / Num. obs: 97136 / % possible obs: 92.2 % / Redundancy: 1.69 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 11.3
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 1.85 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 2.2 / Num. unique all: 9108 / % possible all: 94.8

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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 2ZY4

2zy4


Resolution: 2.65→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2385 4317 -RANDOM
Rwork0.175 ---
all0.178 85058 --
obs0.178 80741 86.7 %-
Solvent computationBsol: 32.773 Å2
Displacement parametersBiso max: 118.92 Å2 / Biso mean: 40.056 Å2 / Biso min: 7.34 Å2
Baniso -1Baniso -2Baniso -3
1-9.694 Å20 Å20 Å2
2---1.975 Å20 Å2
3----7.719 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24224 0 90 1899 26213
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.84378
X-RAY DIFFRACTIONc_bond_d0.01426
LS refinement shellResolution: 2.65→2.74 Å / Rfactor Rfree error: 0.0857
RfactorNum. reflection% reflection
Rfree0.3641 368 -
Rwork0.2784 --
obs-7130 73.22 %

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