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- PDB-6jy1: Crystal Structure of a Group II pyridoxal dependent decarboxylase... -

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Basic information

Entry
Database: PDB / ID: 6jy1
TitleCrystal Structure of a Group II pyridoxal dependent decarboxylase, LLP-bound form from Methanocaldococcus jannaschii at 1.72 A
ComponentsL-tyrosine/L-aspartate decarboxylase
KeywordsLYASE / PLP dependent decarboxylase / Catalytic Domain / Models / Molecular / Protein Conformation / LLP / Tyrosine / Tyrosine Decarboxylase / Structure-Activity Relationship
Function / homology
Function and homology information


methanofuran biosynthetic process / tyrosine decarboxylase / tyrosine decarboxylase activity / sphinganine-1-phosphate aldolase activity / aspartate 1-decarboxylase / aspartate 1-decarboxylase activity / sphingolipid catabolic process / carboxylic acid metabolic process / coenzyme A biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Decarboxylase MfnA, archaea / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase ...Decarboxylase MfnA, archaea / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
L-tyrosine/L-aspartate decarboxylase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsManoj, N. / Gayathri, S.C.
CitationJournal: J.Struct.Biol. / Year: 2019
Title: Structural insights into the mechanism of internal aldimine formation and catalytic loop dynamics in an archaeal Group II decarboxylase.
Authors: Chellam Gayathri, S. / Manoj, N.
History
DepositionApr 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-tyrosine/L-aspartate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4159
Polymers47,6591
Non-polymers7578
Water4,918273
1
A: L-tyrosine/L-aspartate decarboxylase
hetero molecules

A: L-tyrosine/L-aspartate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,83118
Polymers95,3182
Non-polymers1,51316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area12940 Å2
ΔGint-159 kcal/mol
Surface area28550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.580, 98.580, 122.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-541-

HOH

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Components

#1: Protein L-tyrosine/L-aspartate decarboxylase / TDC/ADC


Mass: 47658.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Strain: DSM 2661 / Gene: mfnA, MJ0050 / Plasmid: pSpeedET
Details (production host): Bacterial expression vector, arabinose or T7 induced expression, kanamycin resistance
Production host: Escherichia coli B (bacteria) / Strain (production host): B
References: UniProt: Q60358, aspartate 1-decarboxylase, tyrosine decarboxylase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 3.12 Å3/Da / Density % sol: 60.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 0.1M sodium citrate pH 5.4, 0.2M sodium potassium tartarate, 2.0M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 4, 2015
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.72→51.96 Å / Num. obs: 64532 / % possible obs: 100 % / Redundancy: 8.2 % / Biso Wilson estimate: 23.79 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.024 / Rrim(I) all: 0.071 / Net I/σ(I): 1.72 / Num. measured all: 531270 / Scaling rejects: 1512
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.72-1.758.20.98433730.70.351.047100
9.1-51.966.40.0245120.9750.010.02696.3

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.17data scaling
PDB_EXTRACT3.24data extraction
iMOSFLMv7.1data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F9T

3f9t


Resolution: 1.72→45.716 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.57
RfactorNum. reflection% reflectionSelection details
Rfree0.1883 3191 4.95 %Random
Rwork0.1629 ---
obs0.1641 64440 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 117.74 Å2 / Biso mean: 32.5925 Å2 / Biso min: 11.88 Å2
Refinement stepCycle: final / Resolution: 1.72→45.716 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3091 0 61 273 3425
Biso mean--56.31 36.65 -
Num. residues----390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093224
X-RAY DIFFRACTIONf_angle_d0.9924354
X-RAY DIFFRACTIONf_dihedral_angle_d9.4691946
X-RAY DIFFRACTIONf_chiral_restr0.06481
X-RAY DIFFRACTIONf_plane_restr0.006551
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.72-1.74570.31661400.256726142754100
1.7457-1.7730.24211380.242626032741100
1.773-1.8020.24571390.229426422781100
1.802-1.83310.23431350.210226142749100
1.8331-1.86640.24611500.210426202770100
1.8664-1.90230.24561350.207126442779100
1.9023-1.94120.25781430.216826112754100
1.9412-1.98340.21511470.17626192766100
1.9834-2.02950.18531480.169226182766100
2.0295-2.08030.20771390.173926362775100
2.0803-2.13650.17131210.170226642785100
2.1365-2.19940.16811250.151526552780100
2.1994-2.27040.16531310.162426562787100
2.2704-2.35150.16681370.156526602797100
2.3515-2.44570.18791430.158126512794100
2.4457-2.5570.17351470.14926312778100
2.557-2.69180.17731320.153326792811100
2.6918-2.86040.15721300.159526852815100
2.8604-3.08120.20371420.166926902832100
3.0812-3.39120.19021360.162426972833100
3.3912-3.88160.19131490.135127112860100
3.8816-4.88960.15371420.12827622904100
4.8896-45.73190.1911420.18372887302999

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