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- PDB-6ldr: Structure of a K245A mutant of a Group II PLP dependent decarboxy... -

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Basic information

Entry
Database: PDB / ID: 6ldr
TitleStructure of a K245A mutant of a Group II PLP dependent decarboxylase from Methanocaldococcus jannaschii, in complex with PLP
ComponentsL-tyrosine/L-aspartate decarboxylase
KeywordsLYASE / PLP dependent decarboxylase / Catalytic Domain / Protein Conformation / Pyridoxal 5-phosphate / Lys mutant / Group II 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 / 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 / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
AMMONIUM ION / PYRIDOXAL-5'-PHOSPHATE / L-tyrosine/L-aspartate decarboxylase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsManoj, N. / Gayathri, S.C.
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: Gayathri, S.C. / 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)48,1466
Polymers47,6011
Non-polymers5455
Water5,873326
1
A: L-tyrosine/L-aspartate decarboxylase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)96,29212
Polymers95,2012
Non-polymers1,09110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area11240 Å2
ΔGint-77 kcal/mol
Surface area26550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.380, 98.380, 121.800
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-533-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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 / 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

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Non-polymers , 5 types, 331 molecules

#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.1 Å3/Da / Density % sol: 60.27 %
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: S1 (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.79→49.19 Å / Num. obs: 56951 / % possible obs: 100 % / Redundancy: 9.3 % / Biso Wilson estimate: 23.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.031 / Rrim(I) all: 0.097 / Net I/σ(I): 15.5
Reflection shellResolution: 1.79→1.83 Å / Redundancy: 9.4 % / Rmerge(I) obs: 1.119 / Num. unique obs: 3322 / CC1/2: 0.852 / Rpim(I) all: 0.382 / Rrim(I) all: 1.184 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
Aimless0.6.2data scaling
PDB_EXTRACT3.25data extraction
iMOSFLMv7.1data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JY1

6jy1


Resolution: 1.79→45.82 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1975 2816 5 %Random
Rwork0.169 ---
obs0.1704 56865 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 83.59 Å2 / Biso mean: 28.0014 Å2 / Biso min: 10.54 Å2
Refinement stepCycle: final / Resolution: 1.79→45.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2935 0 76 327 3338
Biso mean--32.29 37.32 -
Num. residues----381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093120
X-RAY DIFFRACTIONf_angle_d0.9924234
X-RAY DIFFRACTIONf_dihedral_angle_d14.0921859
X-RAY DIFFRACTIONf_chiral_restr0.061473
X-RAY DIFFRACTIONf_plane_restr7539
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.79-1.820.24521390.237726772816
1.82-1.850.2751470.229526342781
1.85-1.890.24241540.215726442798
1.89-1.930.2791390.21726612800
1.93-1.970.24751410.194526542795
1.97-2.020.20961550.17926552810
2.02-2.070.1791390.165826602799
2.07-2.120.17611230.166826742797
2.12-2.180.15921320.158327102842
2.18-2.260.17221290.15826742803
2.26-2.340.1911340.15827002834
2.34-2.430.18841480.157126662814
2.43-2.540.19481470.155126892836
2.54-2.670.17491350.161227032838
2.67-2.840.18371290.164227202849
2.84-3.060.21521470.171727062853
3.06-3.370.1921380.168127252863
3.37-3.860.19751490.149127632912
3.86-4.860.16031470.136627842931
4.86-45.820.22891440.208229503094

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