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- PDB-6kho: Crystal structure of Oryza sativa TDC with PLP -

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Basic information

Entry
Database: PDB / ID: 6kho
TitleCrystal structure of Oryza sativa TDC with PLP
ComponentsTryptophan decarboxylase 1
KeywordsLYASE / amino acid decarboxylase / TRANSFERASE
Function / homology
Function and homology information


serotonin biosynthetic process from tryptophan / L-tryptophan decarboxylase activity / 5-hydroxy-L-tryptophan decarboxylase activity / aromatic-L-amino-acid decarboxylase / carboxy-lyase activity / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Aromatic-L-amino-acid decarboxylase / Pyridoxal-phosphate binding site / DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. / 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
ACETATE ION / DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / Tryptophan decarboxylase 1
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.972 Å
AuthorsZhou, Y.Z. / Liao, L.J. / Liu, X.K. / Guo, Y. / Zhao, Y.C. / Zeng, Z.X.
CitationJournal: J Adv Res / Year: 2020
Title: Crystal structure ofOryza sativaTDC reveals the substrate specificity for TDC-mediated melatonin biosynthesis.
Authors: Zhou, Y. / Liao, L. / Liu, X. / Liu, B. / Chen, X. / Guo, Y. / Huang, C. / Zhao, Y. / Zeng, Z.
History
DepositionJul 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tryptophan decarboxylase 1
B: Tryptophan decarboxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,62914
Polymers111,5262
Non-polymers1,10312
Water9,152508
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15860 Å2
ΔGint-128 kcal/mol
Surface area30690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.733, 155.733, 102.182
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Tryptophan decarboxylase 1 / TDC


Mass: 55762.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: TDC1, Os08g0140300, LOC_Os08g04540, OJ1368_G08.14, OsJ_25993
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q6ZJK7, Lyases; Carbon-carbon lyases; Carboxy-lyases

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Non-polymers , 5 types, 520 molecules

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


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 508 / 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: 3.4 Å3/Da / Density % sol: 63.85 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: PEG 1000, Imidazole/Hydrochloric acid, Calcium acetate
PH range: 7.2-8.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Mar 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 98063 / % possible obs: 97.5 % / Redundancy: 9.3 % / Biso Wilson estimate: 33.76 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 39.6
Reflection shellResolution: 1.97→2.03 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 2.476 / Num. unique obs: 9359 / CC1/2: 0.844 / Rsym value: 0.625 / % possible all: 93.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.972→42.717 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.51
RfactorNum. reflection% reflection
Rfree0.1945 4876 4.97 %
Rwork0.1687 --
obs0.1699 98051 97.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.32 Å2 / Biso mean: 37.1049 Å2 / Biso min: 20.45 Å2
Refinement stepCycle: final / Resolution: 1.972→42.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7368 0 64 508 7940
Biso mean--40.51 41.25 -
Num. residues----965
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.972-1.99410.28251800.2532283291
1.9941-2.01750.27752210.222293995
2.0175-2.04210.29161410.2112305696
2.0421-2.0680.2521620.2085304198
2.068-2.09520.22291560.1998311498
2.0952-2.12390.25611700.2068313498
2.1239-2.15420.24991980.1968305298
2.1542-2.18640.24941510.1948312198
2.1864-2.22060.20931590.1875310598
2.2206-2.2570.22111930.1745309899
2.257-2.29590.24041270.1816314399
2.2959-2.33760.22541670.1809309998
2.3376-2.38260.21531360.1834315398
2.3826-2.43120.22471490.1851311999
2.4312-2.48410.21781710.1824311398
2.4841-2.54180.22271680.179282589
2.5418-2.60540.25881610.1825312699
2.6054-2.67580.20491770.1806311699
2.6758-2.75460.21851530.1787314699
2.7546-2.84350.19931490.1738317399
2.8435-2.94510.19081650.1732315499
2.9451-3.06290.21211340.1699320299
3.0629-3.20230.22851660.1776314599
3.2023-3.37110.19261670.16973177100
3.3711-3.58220.17981510.1696315898
3.5822-3.85860.16591630.1548295192
3.8586-4.24660.16191560.14493220100
4.2466-4.86030.161470.14163228100
4.8603-6.12060.1721740.16283231100
6.1206-42.7170.15321640.1541320495

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