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

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Basic information

Entry
Database: PDB / ID: 7cwy
TitleCrystal structure of a tyrosine decarboxylase from Enterococcus faecalis in complex with the cofactor PLP
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-2,4-diaminobutyrate decarboxylase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 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
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


Theoretical massNumber of molelcules
Total (without water)211,0863
Polymers211,0863
Non-polymers00
Water2,846158
1
A: Decarboxylase

A: Decarboxylase


Theoretical massNumber of molelcules
Total (without water)140,7242
Polymers140,7242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area13960 Å2
ΔGint-83 kcal/mol
Surface area38250 Å2
MethodPISA
2
B: Decarboxylase
C: Decarboxylase


Theoretical massNumber of molelcules
Total (without water)140,7242
Polymers140,7242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13990 Å2
ΔGint-90 kcal/mol
Surface area37240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.527, 132.527, 390.130
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-780-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 8 through 417 or resid 428 through 486 or resid 493 through 615))
21(chain B and (resid 8 through 486 or resid 493 through 615))
31(chain C and resid 8 through 615)

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 493 through 615))AA8 - 4178 - 417
12ILEILEPHEPHE(chain A and (resid 8 through 417 or resid 428 through 486 or resid 493 through 615))AA428 - 486428 - 486
13ILEILEGLNGLN(chain A and (resid 8 through 417 or resid 428 through 486 or resid 493 through 615))AA493 - 615493 - 615
21LYSLYSPHEPHE(chain B and (resid 8 through 486 or resid 493 through 615))BB8 - 4868 - 486
22ILEILEGLNGLN(chain B and (resid 8 through 486 or resid 493 through 615))BB493 - 615493 - 615
31LYSLYSGLNGLN(chain C and resid 8 through 615)CC8 - 6158 - 615

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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
Plasmid: pET32 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8KXD2, diaminobutyrate decarboxylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.34 Å3/Da / Density % sol: 47.5 % / Mosaicity: 0.808 °
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: BL13B1 / Wavelength: 0.9998 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2019
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: 2.59→25 Å / Num. obs: 63827 / % possible obs: 99.3 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.031 / Rrim(I) all: 0.105 / Χ2: 1.297 / Net I/σ(I): 9.9 / Num. measured all: 730013
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.59-2.6811.10.84762560.8540.2660.8890.86999.3
2.68-2.7911.50.56862490.9360.1740.5950.89899.2
2.79-2.9211.80.42362600.9620.1280.4420.9599.4
2.92-3.0711.90.31163000.9780.0930.3250.98699.4
3.07-3.2611.80.22563120.9870.0680.2351.07699.5
3.26-3.5111.80.14763460.9940.0440.1541.26899.6
3.51-3.8711.80.09263740.9980.0280.0961.53699.5
3.87-4.4211.50.06364320.9990.0190.0661.75699.4
4.42-5.5611.30.0565060.9990.0160.0521.7999.5
5.56-2510.10.04167920.9990.0140.0441.85498.1

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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: 2.59→24.95 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2479 3173 5 %
Rwork0.1959 60235 -
obs0.1985 63408 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.31 Å2 / Biso mean: 53.1682 Å2 / Biso min: 19.25 Å2
Refinement stepCycle: final / Resolution: 2.59→24.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14294 0 0 158 14452
Biso mean---45.47 -
Num. residues----1799
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5358X-RAY DIFFRACTION6.699TORSIONAL
12B5358X-RAY DIFFRACTION6.699TORSIONAL
13C5358X-RAY DIFFRACTION6.699TORSIONAL
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 (%)
2.59-2.680.33393100.26645900621099
2.68-2.790.33693120.26085914622699
2.79-2.920.33473110.25135926623799
2.92-3.070.29453130.24065942625599
3.07-3.260.32683150.24959576272100
3.26-3.510.28453150.230960076322100
3.51-3.870.26383170.19616019633699
3.87-4.420.22933220.17186075639799
4.42-5.560.20213220.154361536475100
5.56-24.950.17963360.16256342667898

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