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- PDB-7cx0: Crystal structure of a tyrosine decarboxylase from Enterococcus f... -

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Basic information

Entry
Database: PDB / ID: 7cx0
TitleCrystal structure of a tyrosine decarboxylase from Enterococcus faecalis in complex with the cofactor PLP and inhibitor carbidopa
ComponentsDecarboxylaseCarboxy-lyases
KeywordsLYASE / Catalytic / binding pocket / tyrosine decarboxylase
Function / homology
Function and homology information


tyrosine decarboxylase / tyrosine decarboxylase activity / aromatic-L-amino-acid decarboxylase activity / carboxylic acid metabolic process / pyridoxal phosphate binding
Similarity search - Function
: / Tyrosine decarboxylase, C-terminal / Tyrosine decarboxylase, bacteria / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
CARBIDOPA / PYRIDOXAL-5'-PHOSPHATE / Tyrosine decarboxylase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsYu, X. / Gong, M. / Huang, J. / Liu, W. / Chen, C. / Guo, R.
CitationJournal: to be published
Title: Crystal structure of a tyrosine decarboxylase from Enterococcus faecalis in complex with the cofactor PLP and inhibitor carbidopa
Authors: Yu, X. / Gong, M. / Huang, J. / Liu, W. / Chen, C. / Guo, R.
History
DepositionSep 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Decarboxylase
B: Decarboxylase
C: Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,8229
Polymers210,4023
Non-polymers1,4206
Water59433
1
A: Decarboxylase
hetero molecules

A: Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,2156
Polymers140,2682
Non-polymers9474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area15110 Å2
ΔGint-91 kcal/mol
Surface area37200 Å2
MethodPISA
2
B: Decarboxylase
C: Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,2156
Polymers140,2682
Non-polymers9474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15520 Å2
ΔGint-94 kcal/mol
Surface area37190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.696, 131.696, 390.014
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 8 through 111 or resid 113...
21(chain B and (resid 8 through 111 or resid 113...
31(chain C and (resid 8 through 111 or resid 113...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 8 through 111 or resid 113...A8 - 111
121(chain A and (resid 8 through 111 or resid 113...A113 - 417
131(chain A and (resid 8 through 111 or resid 113...A8 - 618
141(chain A and (resid 8 through 111 or resid 113...A449 - 486
151(chain A and (resid 8 through 111 or resid 113...A493 - 615
161(chain A and (resid 8 through 111 or resid 113...A701
211(chain B and (resid 8 through 111 or resid 113...B8 - 111
221(chain B and (resid 8 through 111 or resid 113...B113 - 447
231(chain B and (resid 8 through 111 or resid 113...B449
241(chain B and (resid 8 through 111 or resid 113...B493 - 615
251(chain B and (resid 8 through 111 or resid 113...B701
311(chain C and (resid 8 through 111 or resid 113...C8 - 111
321(chain C and (resid 8 through 111 or resid 113...C113 - 417
331(chain C and (resid 8 through 111 or resid 113...C428 - 447
341(chain C and (resid 8 through 111 or resid 113...C449 - 615
351(chain C and (resid 8 through 111 or resid 113...C701

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Components

#1: Protein Decarboxylase / Carboxy-lyases / Tyrosine decarboxylase


Mass: 70133.977 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria)
Gene: tyrDC, ddc, ELS84_1624, KUB3007_C03520, NCTC8729_00604
Plasmid: pET32 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8KXD2, EC: 4.1.1.86
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-142 / CARBIDOPA / KINSON / 3-(3,4-DIHYDROXY-PHENYL)-2-HYDRAZINO-2-METHYL-PROPIONIC ACID / Carbidopa


Mass: 226.229 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C10H14N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
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: 2.32 Å3/Da / Density % sol: 46.99 % / Mosaicity: 0.898 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 15% PEG 1000, 0.2 M Mgcl2 and 0.1 M sodium citrate tribasic dehydrate (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9998 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jan 27, 2020
RadiationMonochromator: LN2 cooled Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.66→25 Å / Num. obs: 58568 / % possible obs: 99.6 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.033 / Rrim(I) all: 0.113 / Χ2: 1.612 / Net I/σ(I): 8.8 / Num. measured all: 698119
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.66-2.7513.10.84957500.8620.2430.8830.935100
2.75-2.8713.10.62257530.9210.1780.6470.986100
2.87-313.10.4857630.9440.1370.51.064100
3-3.15130.34257790.970.0980.3561.199100
3.15-3.3512.80.25357950.9820.0730.2641.423100
3.35-3.6112.30.16858160.9920.050.1761.833100
3.61-3.9711.80.10658750.9970.0320.112.15499.9
3.97-4.54110.07158890.9980.0220.0742.29899.7
4.54-5.7110.60.05659880.9990.0180.0592.27199.8
5.71-258.70.04661600.9980.0170.0492.53197.1

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HSI

5hsi


Resolution: 2.66→24.89 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2684 2913 5.02 %
Rwork0.2148 55094 -
obs0.2174 58007 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.76 Å2 / Biso mean: 69.9483 Å2 / Biso min: 28.79 Å2
Refinement stepCycle: final / Resolution: 2.66→24.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14090 0 150 33 14273
Biso mean--71.35 58.84 -
Num. residues----1793
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5319X-RAY DIFFRACTION10.11TORSIONAL
12B5319X-RAY DIFFRACTION10.11TORSIONAL
13C5319X-RAY DIFFRACTION10.11TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.66-2.70.34482670.2742439100
2.7-2.750.3944250.28272713100
2.75-2.80.28422713100
2.8-2.850.36642920.28892436100
2.85-2.910.28812706100
2.91-2.980.35652910.28422434100
2.98-3.040.28762742100
3.04-3.120.34022920.27642443100
3.12-3.20.27962744100
3.2-3.30.31962920.27082450100
3.3-3.40.26092723100
3.4-3.530.28312910.24472459100
3.53-3.670.23492766100
3.67-3.830.26192900.20592453100
3.83-4.030.20672758100
4.03-4.290.26052900.20052500100
4.29-4.610.1862278099
4.62-5.080.22922760.18492552100
5.08-5.80.2376150.22812100
5.8-7.280.22191550.1952738100
7.28-24.890.21811370.1588273393

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