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- PDB-4obv: Ruminococcus gnavus tryptophan decarboxylase RUMGNA_01526 (alpha-FMT) -

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Basic information

Entry
Database: PDB / ID: 4obv
TitleRuminococcus gnavus tryptophan decarboxylase RUMGNA_01526 (alpha-FMT)
ComponentsPyridoxal-dependent decarboxylase domain protein
KeywordsLYASE / Type 1 PLP-dependent / Decarboxylase
Function / homology
Function and homology information


L-tryptophan decarboxylase / L-tryptophan decarboxylase activity / tryptophan metabolic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Aspartate Aminotransferase, domain 1 - #170 / 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 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...Aspartate Aminotransferase, domain 1 - #170 / 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 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-(fluoromethyl)-D-tryptophan / Chem-3SO / Tryptophan decarboxylase
Similarity search - Component
Biological speciesRuminococcus gnavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsFraser, J.S. / Van Benschoten, A.H.
CitationJournal: Cell Host Microbe / Year: 2014
Title: Discovery and Characterization of Gut Microbiota Decarboxylases that Can Produce the Neurotransmitter Tryptamine.
Authors: Williams, B.B. / Van Benschoten, A.H. / Cimermancic, P. / Donia, M.S. / Zimmermann, M. / Taketani, M. / Ishihara, A. / Kashyap, P.C. / Fraser, J.S. / Fischbach, M.A.
History
DepositionJan 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Pyridoxal-dependent decarboxylase domain protein
C: Pyridoxal-dependent decarboxylase domain protein
B: Pyridoxal-dependent decarboxylase domain protein
A: Pyridoxal-dependent decarboxylase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,65312
Polymers220,0984
Non-polymers2,5548
Water00
1
D: Pyridoxal-dependent decarboxylase domain protein
B: Pyridoxal-dependent decarboxylase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,3266
Polymers110,0492
Non-polymers1,2774
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12670 Å2
ΔGint-111 kcal/mol
Surface area32180 Å2
MethodPISA
2
C: Pyridoxal-dependent decarboxylase domain protein
A: Pyridoxal-dependent decarboxylase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,3266
Polymers110,0492
Non-polymers1,2774
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12730 Å2
ΔGint-101 kcal/mol
Surface area32620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.030, 135.030, 249.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

#1: Protein
Pyridoxal-dependent decarboxylase domain protein


Mass: 55024.621 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus gnavus (bacteria) / Gene: RUMGNA_01526 / Production host: Escherichia coli (E. coli) / References: UniProt: A7B1V0
#2: Chemical
ChemComp-2SU / alpha-(fluoromethyl)-D-tryptophan


Mass: 236.242 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H13FN2O2
#3: Chemical
ChemComp-3SO / {5-hydroxy-4-[(1E)-4-(1H-indol-3-yl)-3-oxobut-1-en-1-yl]-6-methylpyridin-3-yl}methyl dihydrogen phosphate


Mass: 402.338 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H19N2O6P

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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: 2.59 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.25
Details: 30% ethoxyethanol, 0.1M citrate pH 5.25, 4% polypropylene P400, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 9, 2013
RadiationMonochromator: Double flat crystal, Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 2.84→52.442 Å / Num. all: 55262 / Num. obs: 55229 / % possible obs: 99.94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.84→2.991 Å / % possible all: 99.94

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Processing

Software
NameVersionClassification
Blu-Icedata collection
xia2data scaling
PHENIX(phenix.refine: dev_1260)refinement
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.84→52.442 Å / SU ML: 0.39 / σ(F): 1.34 / Phase error: 24.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2423 1999 3.62 %
Rwork0.2098 --
obs0.211 55229 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.84→52.442 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14821 0 180 0 15001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215424
X-RAY DIFFRACTIONf_angle_d0.54320939
X-RAY DIFFRACTIONf_dihedral_angle_d11.125647
X-RAY DIFFRACTIONf_chiral_restr0.0212320
X-RAY DIFFRACTIONf_plane_restr0.0022653
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.84-2.9110.33451400.2853732X-RAY DIFFRACTION100
2.911-2.98970.36621420.28183775X-RAY DIFFRACTION100
2.9897-3.07770.31411390.27663718X-RAY DIFFRACTION100
3.0777-3.1770.34511410.26713739X-RAY DIFFRACTION100
3.177-3.29060.33231420.25713762X-RAY DIFFRACTION100
3.2906-3.42230.2681410.2553750X-RAY DIFFRACTION100
3.4223-3.5780.26531410.2433758X-RAY DIFFRACTION100
3.578-3.76660.26591420.21263785X-RAY DIFFRACTION100
3.7666-4.00250.24991410.20223782X-RAY DIFFRACTION100
4.0025-4.31140.1911430.17543799X-RAY DIFFRACTION100
4.3114-4.7450.19971430.16353798X-RAY DIFFRACTION100
4.745-5.4310.19521450.17843858X-RAY DIFFRACTION100
5.431-6.84010.22971460.20093894X-RAY DIFFRACTION100
6.8401-52.45110.19581530.18724080X-RAY DIFFRACTION100

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