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- PDB-6khn: Crystal structure of Oryza sativa TDC with PLP and SEROTONIN -

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Basic information

Entry
Database: PDB / ID: 6khn
TitleCrystal structure of Oryza sativa TDC with PLP and SEROTONIN
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 / SEROTONIN / Tryptophan decarboxylase 1
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.293 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)112,68713
Polymers111,5262
Non-polymers1,16111
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15530 Å2
ΔGint-128 kcal/mol
Surface area31030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.274, 156.274, 102.392
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, 345 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-SRO / SEROTONIN / 3-(2-AMINOETHYL)-1H-INDOL-5-OL


Mass: 176.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N2O / Feature type: SUBJECT OF INVESTIGATION / Comment: neurotransmitter*YM
#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


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 0.97846 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Mar 30, 2018
Diffraction measurementDetails: 0.50 degrees, 0.20 sec, detector distance 300.00 mm
Method: \w scans
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97846 Å / Relative weight: 1
ReflectionAv R equivalents: 0.102 / Number: 518804
ReflectionResolution: 2.293→50 Å / Num. obs: 64622 / % possible obs: 99.9 % / Redundancy: 8 % / Biso Wilson estimate: 36.49 Å2 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.038 / Rrim(I) all: 0.109 / Χ2: 1.857 / Net I/σ(I): 12.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.387.50.71264120.8910.2780.7660.621100
2.38-2.487.10.54663810.9250.2190.590.68999.9
2.48-2.597.10.42563980.9470.1720.4590.75799.8
2.59-2.738.10.33964080.9730.1280.3630.85999.9
2.73-2.98.10.25264480.9810.0950.2691.094100
2.9-3.128.20.18264530.9880.0680.1951.49899.9
3.12-3.448.20.12864270.9930.0480.1372.0799.9
3.44-3.9380.08764660.9970.0330.0933.07999.8
3.93-4.9590.06665200.9970.0230.073.65499.9
4.95-508.80.05267090.9980.0180.0553.34999.9
Cell measurementReflection used: 518804

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.293→47.884 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.25
RfactorNum. reflection% reflection
Rfree0.2018 3161 4.89 %
Rwork0.1628 --
obs0.1646 64580 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.93 Å2 / Biso mean: 39.3799 Å2 / Biso min: 23 Å2
Refinement stepCycle: final / Resolution: 2.293→47.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7372 0 69 334 7775
Biso mean--49.87 41.53 -
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 (%)
2.2932-2.32740.27131380.2036256796
2.3274-2.36380.25181160.2042673100
2.3638-2.40250.24291430.2022621100
2.4025-2.4440.28521520.20012639100
2.444-2.48840.23491500.20092644100
2.4884-2.53630.23131470.19822624100
2.5363-2.5880.27121300.19352651100
2.588-2.64430.2761250.1932660100
2.6443-2.70580.21451490.18582662100
2.7058-2.77350.2361340.18212630100
2.7735-2.84840.24071400.18252684100
2.8484-2.93230.24221480.18372639100
2.9323-3.02690.21631410.18222664100
3.0269-3.1350.22941170.182683100
3.135-3.26050.22541560.17552653100
3.2605-3.40890.21641500.17732674100
3.4089-3.58860.2081320.17412663100
3.5886-3.81330.17461270.14842709100
3.8133-4.10760.1861290.14262679100
4.1076-4.52070.16731100.12972726100
4.5207-5.17420.15051450.13272710100
5.1742-6.51630.18841740.16452693100
6.5163-47.8840.14061080.13692871100

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