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- PDB-6khp: Crystal structure of Oryza sativa TDC with PLP and tryptamine -

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Basic information

Entry
Database: PDB / ID: 6khp
TitleCrystal structure of Oryza sativa TDC with PLP and tryptamine
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 / 2-(1H-INDOL-3-YL)ETHANAMINE / Tryptophan decarboxylase 1
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.299 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)112,67113
Polymers111,5262
Non-polymers1,14511
Water7,368409
1
A: Tryptophan decarboxylase 1
B: Tryptophan decarboxylase 1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)225,34226
Polymers223,0524
Non-polymers2,29022
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area33300 Å2
ΔGint-269 kcal/mol
Surface area58920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.769, 155.769, 102.094
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 , 6 types, 420 molecules

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


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TSS / 2-(1H-INDOL-3-YL)ETHANAMINE / TRYPTAMINE


Mass: 160.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 409 / 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: 63.82 %
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: SSRF / Beamline: BL19U1 / Wavelength: 0.91905 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Jan 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91905 Å / Relative weight: 1
ReflectionResolution: 2.29→28.139 Å / Num. obs: 63568 / % possible obs: 99.8 % / Redundancy: 15.9 % / Biso Wilson estimate: 31.61 Å2 / Rmerge(I) obs: 0.116 / Rsym value: 0.116 / Net I/σ(I): 15.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 6273 / Rsym value: 0.717 / % possible all: 99.6

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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: 2.299→28.139 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.79
RfactorNum. reflection% reflection
Rfree0.1978 3160 4.97 %
Rwork0.163 --
obs0.1648 63528 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.99 Å2 / Biso mean: 35.7468 Å2 / Biso min: 17.76 Å2
Refinement stepCycle: final / Resolution: 2.299→28.139 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7372 0 68 409 7849
Biso mean--42.04 37.27 -
Num. residues----966
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.299-2.33320.2771350.2278260499
2.3332-2.36970.26441110.20182603100
2.3697-2.40850.24931180.1932597100
2.4085-2.450.24781450.18952630100
2.45-2.49450.25281110.19392605100
2.4945-2.54250.21911390.19012640100
2.5425-2.59430.22661450.18012575100
2.5943-2.65070.20491470.17982591100
2.6507-2.71230.19791090.17132633100
2.7123-2.78010.21311370.17542648100
2.7801-2.85520.22931490.17942575100
2.8552-2.93910.2511490.18382595100
2.9391-3.03390.21621590.1766258899
3.0339-3.14220.22631280.1823260399
3.1422-3.26780.20921570.17872618100
3.2678-3.41630.20711290.18152628100
3.4163-3.5960.2181420.17442627100
3.596-3.82080.18451290.14862635100
3.8208-4.1150.18731500.14182628100
4.115-4.52760.15581380.12782655100
4.5276-5.17920.14831370.12982672100
5.1792-6.51190.19451450.16052670100
6.5119-28.1390.14691510.1398274899

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