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- PDB-6m4y: Structure of a R371A mutant of a Group II PLP dependent decarboxy... -

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Basic information

Entry
Database: PDB / ID: 6m4y
TitleStructure of a R371A mutant of a Group II PLP dependent decarboxylase from Methanocaldococcus jannaschii
ComponentsL-tyrosine/L-aspartate decarboxylase
KeywordsLYASE / PLP dependent decarboxylase / Catalytic mutant / Protein Conformation / LLP / internal aldimine / Tyrosine / Tyrosine Decarboxylase / Structure-Activity Relationship
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
L-tyrosine/L-aspartate decarboxylase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsManoj, N. / Chellam Gayathri, S.
Citation
Journal: J.Mol.Biol. / Year: 2020
Title: Crystallographic Snapshots of the Dunathan and Quinonoid Intermediates provide Insights into the Reaction Mechanism of Group II Decarboxylases.
Authors: Gayathri, S.C. / 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
DepositionMar 9, 2020Deposition 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 29, 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)48,1417
Polymers47,5731
Non-polymers5686
Water5,098283
1
A: L-tyrosine/L-aspartate decarboxylase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)96,28214
Polymers95,1452
Non-polymers1,13712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area11390 Å2
ΔGint-136 kcal/mol
Surface area27590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.440, 98.440, 121.700
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-584-

HOH

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Components

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


Mass: 47572.715 Da / Num. of mol.: 1 / Mutation: R371A
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 / Plasmid: pSpeedET / Details (production host): Bacterial expression vector / Production host: Escherichia coli B (bacteria) / Strain (production host): B
References: UniProt: Q60358, aspartate 1-decarboxylase, tyrosine decarboxylase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.16 Å3/Da / Density % sol: 61.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M sodium citrate pH 5.4, 0.2M sodium potassium tartarate, 2.0M ammonium sulphate
PH range: 5.4-5.6

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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: Aug 20, 2017
RadiationMonochromator: Double mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→38.27 Å / Num. obs: 35618 / % possible obs: 100 % / Redundancy: 26.5 % / Biso Wilson estimate: 24.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.208 / Rpim(I) all: 0.041 / Rrim(I) all: 0.212 / Net I/σ(I): 16.7
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 25.9 % / Rmerge(I) obs: 1.202 / Num. unique obs: 2856 / CC1/2: 0.851 / Rpim(I) all: 0.24 / Rrim(I) all: 1.226 / % possible all: 100

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Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
PHENIX1.17_3644refinement
PDB_EXTRACT3.25data extraction
iMOSFLMv7.1data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JY1

6jy1


Resolution: 2.1→38.27 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.1
RfactorNum. reflection% reflectionSelection details
Rfree0.2001 1715 5 %RANDOM
Rwork0.1636 ---
obs0.1653 35550 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.09 Å2 / Biso mean: 30.1142 Å2 / Biso min: 10.3 Å2
Refinement stepCycle: final / Resolution: 2.1→38.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2984 0 38 283 3305
Biso mean--52.99 36.68 -
Num. residues----389
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013117
X-RAY DIFFRACTIONf_angle_d0.9994226
X-RAY DIFFRACTIONf_dihedral_angle_d12.711859
X-RAY DIFFRACTIONf_chiral_restr0.06477
X-RAY DIFFRACTIONf_plane_restr0.006535
LS refinement shellResolution: 2.1→2.16 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2091 125 -
Rwork0.1779 2774 -
obs--100 %

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