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- PDB-6ldt: K245A mutant of L-tyrosine decarboxylase from Methanocaldococcus ... -

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Basic information

Entry
Database: PDB / ID: 6ldt
TitleK245A mutant of L-tyrosine decarboxylase from Methanocaldococcus jannaschii complexed with a post-decarboxylation quinonoid-like intermediate formed with L-tyrosine
ComponentsL-tyrosine/L-aspartate decarboxylase
KeywordsLYASE / PLP dependent decarboxylase / Catalytic Domain / Models / Molecular / Protein Conformation / PLP / Tyrosine / Quinonoid / Tyrosine Decarboxylase / Structure-Activity Relationship / Dunathan alignment
Function / homology
Function and homology information


methanofuran biosynthetic process / tyrosine decarboxylase / tyrosine decarboxylase activity / aspartate 1-decarboxylase / aspartate 1-decarboxylase activity / coenzyme A biosynthetic process / carboxylic acid metabolic process / pyridoxal phosphate binding
Similarity search - Function
Decarboxylase MfnA, archaea / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-EBR / L-tyrosine/L-aspartate decarboxylase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsManoj, N. / Chellam Gayathri, S.
Citation
Journal: 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.
#1: Journal: 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
DepositionNov 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
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)48,3396
Polymers47,6011
Non-polymers7395
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)96,67912
Polymers95,2012
Non-polymers1,47710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area10310 Å2
ΔGint-77 kcal/mol
Surface area26980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.370, 98.370, 121.720
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-516-

HOH

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Components

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


Mass: 47600.730 Da / Num. of mol.: 1 / Mutation: K245A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: mfnA, MJ0050 / Production host: Escherichia coli B (bacteria) / Strain (production host): B
References: UniProt: Q60358, aspartate 1-decarboxylase, tyrosine decarboxylase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EBR / [(4Z)-4-[[(Z)-2-(4-hydroxyphenyl)ethylideneamino]methylidene]-6-methyl-5-oxidanyl-1H-pyridin-3-yl]methyl dihydrogen phosphate


Mass: 366.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19N2O6P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.3 Å3/Da / Density % sol: 62.8 %
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: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 14, 2015
RadiationMonochromator: Double mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→38.25 Å / Num. obs: 45548 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 25.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.037 / Rrim(I) all: 0.134 / Net I/σ(I): 14.1
Reflection shellResolution: 1.93→1.98 Å / Redundancy: 11.8 % / Rmerge(I) obs: 1.142 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2993 / CC1/2: 0.716 / Rpim(I) all: 0.342 / Rrim(I) all: 1.193 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.25data extraction
iMOSFLMv7.1data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LDR

6ldr


Resolution: 1.93→38.25 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.12
RfactorNum. reflection% reflectionSelection details
Rfree0.2266 2229 5 %RANDOM
Rwork0.1879 ---
obs0.1898 45424 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 65.29 Å2 / Biso mean: 27.8448 Å2 / Biso min: 10.82 Å2
Refinement stepCycle: final / Resolution: 1.93→38.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2922 0 48 273 3243
Biso mean--33.17 35.69 -
Num. residues----382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063033
X-RAY DIFFRACTIONf_angle_d0.7644105
X-RAY DIFFRACTIONf_dihedral_angle_d12.2681808
X-RAY DIFFRACTIONf_chiral_restr0.055464
X-RAY DIFFRACTIONf_plane_restr0.005536
LS refinement shellResolution: 1.93→1.97 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2914 145 -
Rwork0.2454 2616 -
obs--100 %

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