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

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Basic information

Entry
Database: PDB / ID: 7cwx
TitleCrystal structure of a tyrosine decarboxylase from Enterococcus faecalis
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
DI(HYDROXYETHYL)ETHER / L-2,4-diaminobutyrate decarboxylase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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
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)210,7066
Polymers210,4023
Non-polymers3043
Water10,611589
1
A: Decarboxylase
hetero molecules

A: Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,4804
Polymers140,2682
Non-polymers2122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area14500 Å2
ΔGint-86 kcal/mol
Surface area39050 Å2
MethodPISA
2
B: Decarboxylase
C: Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,4664
Polymers140,2682
Non-polymers1982
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14220 Å2
ΔGint-85 kcal/mol
Surface area38680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.338, 132.338, 391.483
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 429...
21(chain B and (resid 8 through 484 or resid 496 through 535 or resid 539 through 612))
31(chain C and (resid 8 through 417 or resid 429 through 612))

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 429...AA8 - 4178 - 417
12PROPROLEULEU(chain A and (resid 8 through 417 or resid 429...AA429 - 484429 - 484
13HISHISHISHIS(chain A and (resid 8 through 417 or resid 429...AA496496
21LYSLYSLEULEU(chain B and (resid 8 through 484 or resid 496 through 535 or resid 539 through 612))BB8 - 4848 - 484
22HISHISVALVAL(chain B and (resid 8 through 484 or resid 496 through 535 or resid 539 through 612))BB496 - 535496 - 535
23ILEILELYSLYS(chain B and (resid 8 through 484 or resid 496 through 535 or resid 539 through 612))BB539 - 612539 - 612
31LYSLYSPHEPHE(chain C and (resid 8 through 417 or resid 429 through 612))CC8 - 4178 - 417
32PROPROLYSLYS(chain C and (resid 8 through 417 or resid 429 through 612))CC429 - 612429 - 612

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Components

#1: Protein Decarboxylase / 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, diaminobutyrate decarboxylase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 589 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.35 Å3/Da / Density % sol: 47.7 % / Mosaicity: 0.808 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 15% PEG 1000, 0.2 M Mgcl2, 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: 2.15→25 Å / Num. obs: 110354 / % possible obs: 99.6 % / Redundancy: 21.6 % / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.023 / Rrim(I) all: 0.104 / Χ2: 0.834 / Net I/σ(I): 5.8 / Num. measured all: 2388870
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.15-2.2316.9107940.8510.2610.50499.2
2.23-2.3220.1108320.9250.1850.51599.30.8630.883
2.32-2.4221.4108240.960.1370.52499.40.6560.671
2.42-2.5522.2108930.9780.0980.5499.50.4720.482
2.55-2.7123109100.9890.0670.55999.60.3220.329
2.71-2.9223.1109490.9960.040.61899.70.1950.199
2.92-3.2123.1110240.9980.0270.72899.80.1310.134
3.21-3.6722.9111190.9990.0181.08899.90.0890.091
3.67-4.6222.6112140.9990.0121.49999.90.0590.06
4.62-2521.11179510.011.59299.70.0460.047

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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: 2.15→24.96 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2297 5502 5 %
Rwork0.1921 104561 -
obs0.194 110063 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.75 Å2 / Biso mean: 43.4972 Å2 / Biso min: 13.07 Å2
Refinement stepCycle: final / Resolution: 2.15→24.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14199 0 20 589 14808
Biso mean--49.38 43.76 -
Num. residues----1784
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5232X-RAY DIFFRACTION5.977TORSIONAL
12B5232X-RAY DIFFRACTION5.977TORSIONAL
13C5232X-RAY DIFFRACTION5.977TORSIONAL
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 (%)
2.15-2.230.28795380.2325102271076599
2.23-2.320.27525410.2157102881082999
2.32-2.420.28725400.2151026410804100
2.42-2.550.26075450.20641035510900100
2.55-2.710.28025450.20911034010885100
2.71-2.920.24795480.19691040610954100
2.92-3.210.2555500.20541045711007100
3.21-3.670.2355560.1941055211108100
3.67-4.620.18475590.1631063711196100
4.62-24.960.20315800.1874110351161599

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