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- PDB-7cx1: Crystal structure of a tyrosine decarboxylase from Enterococcus f... -

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Basic information

Entry
Database: PDB / ID: 7cx1
TitleCrystal structure of a tyrosine decarboxylase from Enterococcus faecalis in complex with the cofactor PLP and inhibitor methyl-tyrosine
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
4-[(2R)-2-(methylamino)propyl]phenol / L-2,4-diaminobutyrate decarboxylase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 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 methyl-tyrosine
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)211,7477
Polymers211,0863
Non-polymers6614
Water3,693205
1
A: Decarboxylase
hetero molecules

A: Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,0554
Polymers140,7242
Non-polymers3302
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area13970 Å2
ΔGint-83 kcal/mol
Surface area36680 Å2
MethodPISA
2
B: Decarboxylase
C: Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,2205
Polymers140,7242
Non-polymers4963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14230 Å2
ΔGint-89 kcal/mol
Surface area36740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.490, 131.490, 385.660
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 417 or resid 428 through 486 or resid 494 through 615 or resid 701))
21(chain B and (resid 8 through 486 or resid 494 through 615 or resid 1101))
31(chain C and (resid 8 through 417 or resid 428 through 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
11LYSLYSPHEPHE(chain A and (resid 8 through 417 or resid 428 through 486 or resid 494 through 615 or resid 701))AA8 - 4178 - 417
12ILEILEPHEPHE(chain A and (resid 8 through 417 or resid 428 through 486 or resid 494 through 615 or resid 701))AA428 - 486428 - 486
13GLUGLUGLNGLN(chain A and (resid 8 through 417 or resid 428 through 486 or resid 494 through 615 or resid 701))AA494 - 615494 - 615
14GKUGKUGKUGKU(chain A and (resid 8 through 417 or resid 428 through 486 or resid 494 through 615 or resid 701))AD701
21LYSLYSPHEPHE(chain B and (resid 8 through 486 or resid 494 through 615 or resid 1101))BB8 - 4868 - 486
22GLUGLUGLNGLN(chain B and (resid 8 through 486 or resid 494 through 615 or resid 1101))BB494 - 615494 - 615
23GKUGKUGKUGKU(chain B and (resid 8 through 486 or resid 494 through 615 or resid 1101))BE1101
31LYSLYSPHEPHE(chain C and (resid 8 through 417 or resid 428 through 701))CC8 - 4178 - 417
32ILEILEGKUGKU(chain C and (resid 8 through 417 or resid 428 through 701))CC - G428 - 701428

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Components

#1: Protein Decarboxylase / Tyrosine decarboxylase


Mass: 70362.094 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
Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8KXD2, diaminobutyrate decarboxylase
#2: Chemical
ChemComp-GKU / 4-[(2R)-2-(methylamino)propyl]phenol


Mass: 165.232 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15NO / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting 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: 2.54→25 Å / Num. obs: 65687 / % possible obs: 100 % / Redundancy: 29 % / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.029 / Rrim(I) all: 0.153 / Χ2: 0.639 / Net I/σ(I): 3.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.75-2.8527.91.09452670.9020.2091.1140.316100
2.85-2.9630.30.79452940.9450.1460.8080.336100
2.96-3.130.40.58752980.9680.1080.5970.368100
3.1-3.2630.30.42653130.9810.0780.4340.409100
3.26-3.4630.20.27653320.9910.0510.2810.468100
3.46-3.7329.90.17453600.9970.0320.1770.57100
3.73-4.129.50.12453910.9980.0230.1260.746100
4.1-4.6928.90.10954350.9980.0210.1111.112100
4.69-5.9280.155130.9980.0190.1021.149100
5.9-25250.0558400.9990.010.0510.95299.9

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Processing

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

5hsi


Resolution: 2.54→24.85 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.253 3283 5 %
Rwork0.2099 62404 -
obs0.2121 65687 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.46 Å2 / Biso mean: 48.8118 Å2 / Biso min: 21.63 Å2
Refinement stepCycle: final / Resolution: 2.54→24.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14185 0 108 205 14498
Biso mean--54.2 30 -
Num. residues----1795
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5346X-RAY DIFFRACTION12.281TORSIONAL
12B5346X-RAY DIFFRACTION12.281TORSIONAL
13C5346X-RAY DIFFRACTION12.281TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.54-2.630.36653220.298561196441
2.63-2.740.31643220.278460956417
2.74-2.860.33143240.274661386462
2.86-3.010.35113200.268361256445
3.01-3.20.31953250.270561876512
3.2-3.450.2913270.244762056532
3.45-3.790.23723260.208562176543
3.79-4.340.22193280.181762516579
4.34-5.450.20193360.166163686704
5.46-24.850.20673530.166266997052

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