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

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Basic information

Entry
Database: PDB / ID: 7cwz
TitleCrystal structure of a tyrosine decarboxylase from Enterococcus faecalis K392A mutant in complex with the cofactor PLP and L-dopa
ComponentsDecarboxylase
KeywordsLYASE / Catalytic / binding pocket / tyrosine decarboxylase
Function / homology
Function and homology information


diaminobutyrate decarboxylase / tyrosine decarboxylase / tyrosine decarboxylase activity / aromatic-L-amino-acid decarboxylase activity / carboxylic acid metabolic process / pyridoxal phosphate binding
Similarity search - Function
Tyrosine decarboxylase, bacteria / : / Tyrosine decarboxylase, C-terminal / : / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
L-DOPAMINE / PYRIDOXAL-5'-PHOSPHATE / L-2,4-diaminobutyrate decarboxylase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 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 K392A mutant in complex with the cofactor PLP and L-dopa
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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)211,47711
Polymers210,2283
Non-polymers1,2508
Water1,00956
1
A: Decarboxylase
hetero molecules

A: Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,0018
Polymers140,1522
Non-polymers8496
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area15970 Å2
ΔGint-90 kcal/mol
Surface area37160 Å2
MethodPISA
2
B: Decarboxylase
C: Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,9777
Polymers140,1522
Non-polymers8255
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16370 Å2
ΔGint-84 kcal/mol
Surface area37870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.314, 133.314, 390.631
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 201 or resid 203...
21(chain B and (resid 8 through 429 or resid 433...
31(chain C and (resid 8 through 201 or resid 203 through 429 or resid 433 through 616 or resid 701))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSLYSLYS(chain A and (resid 8 through 201 or resid 203...AA8 - 2018 - 201
12ILEILEPHEPHE(chain A and (resid 8 through 201 or resid 203...AA203 - 417203 - 417
13ILEILEILEILE(chain A and (resid 8 through 201 or resid 203...AA428428
14LYSLYSASPASP(chain A and (resid 8 through 201 or resid 203...AA8 - 6188 - 618
15LYSLYSASPASP(chain A and (resid 8 through 201 or resid 203...AA8 - 6188 - 618
16LYSLYSASPASP(chain A and (resid 8 through 201 or resid 203...AA8 - 6188 - 618
17LYSLYSASPASP(chain A and (resid 8 through 201 or resid 203...AA8 - 6188 - 618
18LYSLYSASPASP(chain A and (resid 8 through 201 or resid 203...AA8 - 6188 - 618
19LYSLYSASPASP(chain A and (resid 8 through 201 or resid 203...AA8 - 6188 - 618
21LYSLYSPROPRO(chain B and (resid 8 through 429 or resid 433...BB8 - 4298 - 429
22GLYGLYGLYGLY(chain B and (resid 8 through 429 or resid 433...BB433 - 489433 - 489
23ASPASPASPASP(chain B and (resid 8 through 429 or resid 433...BB490490
24LEULEUASPASP(chain B and (resid 8 through 429 or resid 433...BB6 - 6186 - 618
25LEULEUASPASP(chain B and (resid 8 through 429 or resid 433...BB6 - 6186 - 618
26LEULEUASPASP(chain B and (resid 8 through 429 or resid 433...BB6 - 6186 - 618
27LEULEUASPASP(chain B and (resid 8 through 429 or resid 433...BB6 - 6186 - 618
31LYSLYSLYSLYS(chain C and (resid 8 through 201 or resid 203 through 429 or resid 433 through 616 or resid 701))CC8 - 2018 - 201
32ILEILEPROPRO(chain C and (resid 8 through 201 or resid 203 through 429 or resid 433 through 616 or resid 701))CC203 - 429203 - 429
33GLYGLYILEILE(chain C and (resid 8 through 201 or resid 203 through 429 or resid 433 through 616 or resid 701))CC433 - 616433 - 616
34PLPPLPPLPPLP(chain C and (resid 8 through 201 or resid 203 through 429 or resid 433 through 616 or resid 701))CJ701

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Components

#1: Protein Decarboxylase / Tyrosine decarboxylase


Mass: 70075.875 Da / Num. of mol.: 3 / Mutation: K392A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria)
Gene: tyrDC, ddc, ELS84_1624, KUB3007_C03520, NCTC8729_00604
Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8KXD2, diaminobutyrate decarboxylase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-LDP / L-DOPAMINE / DOPAMINE


Mass: 153.178 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H11NO2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.38 Å3/Da / Density % sol: 48.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
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: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 2.97→25 Å / Num. obs: 43434 / % possible obs: 99.9 % / Redundancy: 16.9 % / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.043 / Rrim(I) all: 0.179 / Χ2: 1.03 / Net I/σ(I): 5.7 / Num. measured all: 732993
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.97-3.0813.71.14842060.9240.3131.1910.82599.9
3.08-3.215.91.07342600.9480.2731.1070.83699.9
3.2-3.3417.30.81342520.9720.1980.8370.86299.9
3.34-3.52180.55142730.9880.1320.5670.934100
3.52-3.74180.32842750.9930.0790.3371.022100
3.74-4.0317.90.20543020.9970.050.2111.09299.9
4.03-4.4317.70.1543420.9970.0360.1541.171100
4.43-5.0717.50.1243600.9960.0290.1231.33100
5.07-6.37170.10144590.9970.0250.1041.158100
6.37-2515.80.04647050.9990.0120.0470.9999.7

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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: 2.97→24.85 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2935 2139 5.04 %
Rwork0.2426 40342 -
obs0.2452 42481 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.04 Å2 / Biso mean: 52.568 Å2 / Biso min: 22.92 Å2
Refinement stepCycle: final / Resolution: 2.97→24.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14087 0 131 56 14274
Biso mean--57.01 30.08 -
Num. residues----1794
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5383X-RAY DIFFRACTION8.612TORSIONAL
12B5383X-RAY DIFFRACTION8.612TORSIONAL
13C5383X-RAY DIFFRACTION8.612TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.97-3.080.40952160.33643685390193
3.08-3.20.42442160.334440054221100
3.2-3.340.40142150.310740344249100
3.34-3.520.40452150.29484025424099
3.52-3.740.31852100.25763983419399
3.74-4.030.27432120.23943990420298
4.03-4.430.25862140.22034025423998
4.43-5.070.25522110.2034047425898
5.07-6.370.27572140.22564183439799
6.37-24.850.21132160.20224365458198

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