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- PDB-4obu: Ruminococcus gnavus tryptophan decarboxylase RUMGNA_01526 (apo) -

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Basic information

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


L-tryptophan decarboxylase / L-tryptophan decarboxylase activity / L-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
PYRIDOXAL-5'-PHOSPHATE / Tryptophan decarboxylase
Similarity search - Component
Biological speciesRuminococcus gnavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.804 Å
AuthorsVan Benschoten, A.H. / Fraser, J.S.
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

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Assembly

Deposited unit
E: Pyridoxal-dependent decarboxylase domain protein
A: Pyridoxal-dependent decarboxylase domain protein
U: Pyridoxal-dependent decarboxylase domain protein
G: Pyridoxal-dependent decarboxylase domain protein
H: Pyridoxal-dependent decarboxylase domain protein
F: Pyridoxal-dependent decarboxylase domain protein
B: Pyridoxal-dependent decarboxylase domain protein
C: Pyridoxal-dependent decarboxylase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)442,17416
Polymers440,1978
Non-polymers1,9778
Water7,458414
1
E: Pyridoxal-dependent decarboxylase domain protein
H: Pyridoxal-dependent decarboxylase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,5444
Polymers110,0492
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13720 Å2
ΔGint-104 kcal/mol
Surface area33010 Å2
MethodPISA
2
A: Pyridoxal-dependent decarboxylase domain protein
hetero molecules

U: Pyridoxal-dependent decarboxylase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,5444
Polymers110,0492
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area13720 Å2
ΔGint-105 kcal/mol
Surface area33110 Å2
MethodPISA
3
F: Pyridoxal-dependent decarboxylase domain protein
hetero molecules

G: Pyridoxal-dependent decarboxylase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,5444
Polymers110,0492
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area13680 Å2
ΔGint-104 kcal/mol
Surface area33140 Å2
MethodPISA
4
B: Pyridoxal-dependent decarboxylase domain protein
C: Pyridoxal-dependent decarboxylase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,5444
Polymers110,0492
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13700 Å2
ΔGint-104 kcal/mol
Surface area33080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.630, 145.770, 165.070
Angle α, β, γ (deg.)72.85, 88.84, 88.30
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Pyridoxal-dependent decarboxylase domain protein


Mass: 55024.621 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus gnavus (bacteria) / Strain: ATCC 29149 / Gene: RUMGNA_01526 / Production host: Escherichia coli (E. coli) / References: UniProt: A7B1V0
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / Source method: isolated from a natural source / Formula: H2O

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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: 3.06 Å3/Da / Density % sol: 59.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Bicine pH 8.5, 25% PEG 3350, 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: Sep 30, 2012
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: 2.804→79.37 Å / Num. all: 127885 / Num. obs: 121043 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.804→2.905 Å / % possible all: 96.28

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Processing

Software
NameVersionClassification
Blu-Icedata collection
xia2data scaling
PHENIX(phenix.refine: 1.8.1_1168)refinement
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.804→79.369 Å / SU ML: 0.4 / σ(F): 1.97 / Phase error: 27.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2568 6082 5.02 %Random
Rwork0.2311 ---
obs0.2324 121043 94.65 %-
all-127885 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.804→79.369 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29064 0 120 414 29598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00229824
X-RAY DIFFRACTIONf_angle_d0.6740424
X-RAY DIFFRACTIONf_dihedral_angle_d11.84110896
X-RAY DIFFRACTIONf_chiral_restr0.0494528
X-RAY DIFFRACTIONf_plane_restr0.0035144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8044-2.83630.36372120.30863831X-RAY DIFFRACTION96
2.8363-2.86970.35841910.29893876X-RAY DIFFRACTION96
2.8697-2.90470.35642000.29433952X-RAY DIFFRACTION96
2.9047-2.94140.34621610.3033981X-RAY DIFFRACTION96
2.9414-2.98020.34072010.29073839X-RAY DIFFRACTION96
2.9802-3.0210.34652270.29633827X-RAY DIFFRACTION96
3.021-3.06410.34722180.29543895X-RAY DIFFRACTION96
3.0641-3.10990.34112080.29493962X-RAY DIFFRACTION96
3.1099-3.15850.31582200.27663806X-RAY DIFFRACTION96
3.1585-3.21030.28911950.26973894X-RAY DIFFRACTION96
3.2103-3.26560.33042200.27663916X-RAY DIFFRACTION95
3.2656-3.3250.29732220.25673790X-RAY DIFFRACTION96
3.325-3.3890.29131960.25233855X-RAY DIFFRACTION95
3.389-3.45810.27592330.24543901X-RAY DIFFRACTION95
3.4581-3.53330.27142090.23943785X-RAY DIFFRACTION95
3.5333-3.61550.23652140.23493835X-RAY DIFFRACTION95
3.6155-3.70590.26831890.22983771X-RAY DIFFRACTION93
3.7059-3.80610.25222050.21693821X-RAY DIFFRACTION95
3.8061-3.91810.23012060.21863867X-RAY DIFFRACTION94
3.9181-4.04460.2182220.21043745X-RAY DIFFRACTION94
4.0446-4.18910.23391910.20863894X-RAY DIFFRACTION94
4.1891-4.35690.23042070.20743694X-RAY DIFFRACTION94
4.3569-4.55510.21791890.20323904X-RAY DIFFRACTION94
4.5551-4.79520.20251840.19243737X-RAY DIFFRACTION93
4.7952-5.09560.20981960.19843822X-RAY DIFFRACTION94
5.0956-5.4890.23281930.2023803X-RAY DIFFRACTION94
5.489-6.04120.2391950.21853762X-RAY DIFFRACTION93
6.0412-6.91490.22052000.21473743X-RAY DIFFRACTION93
6.9149-8.71030.20382020.18753826X-RAY DIFFRACTION94
8.7103-79.40060.19991760.19993627X-RAY DIFFRACTION89

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