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- PDB-8jg7: Serine decarboxylase -

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Basic information

Entry
Database: PDB / ID: 8jg7
TitleSerine decarboxylase
ComponentsSerine decarboxylase
KeywordsBIOSYNTHETIC PROTEIN / PLP
Function / homology
Function and homology information


serine decarboxylase activity / ethanolamine metabolic process / Lyases; Carbon-carbon lyases; Carboxy-lyases / carboxylic acid metabolic process / pyridoxal phosphate binding / plasma membrane / cytosol
Similarity search - Function
: / Pyridoxal-phosphate binding site / DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Serine decarboxylase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsWang, H. / Gong, W.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: Elife / Year: 2024
Title: Structure and evolution of alanine/serine decarboxylases and the engineering of theanine production.
Authors: Wang, H. / Zhu, B. / Qiao, S. / Dong, C. / Wan, X. / Gong, W. / Zhang, Z.
History
DepositionMay 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine decarboxylase
C: Serine decarboxylase
D: Serine decarboxylase
E: Serine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,36416
Polymers189,7454
Non-polymers1,61912
Water00
1
A: Serine decarboxylase
E: Serine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6828
Polymers94,8722
Non-polymers8096
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9870 Å2
ΔGint-53 kcal/mol
Surface area31050 Å2
MethodPISA
2
C: Serine decarboxylase
D: Serine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6828
Polymers94,8722
Non-polymers8096
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9850 Å2
ΔGint-54 kcal/mol
Surface area31120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.360, 149.450, 139.126
Angle α, β, γ (deg.)90.00, 109.18, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Serine decarboxylase / AtSDC / Protein EMBRYO DEFECTIVE 1075 / Serine decarboxylase 1 / AtSDC1


Mass: 47436.230 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SDC, EMB1075, SDC1, At1g43710, F2J6.7 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9MA74, Lyases; Carbon-carbon lyases; Carboxy-lyases
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
Has ligand of interestY
Has protein modificationN

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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: 2.99 Å3/Da / Density % sol: 58.85 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 400, 0.2M CaCl2, PH8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 52125 / % possible obs: 99.6 % / Redundancy: 5.9 % / CC1/2: 0.86 / CC star: 0.962 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.076 / Rrim(I) all: 0.189 / Χ2: 2.023 / Net I/σ(I): 3.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.85-2.950.55125560.8460.9570.270.6160.54598.1
2.9-2.955.70.54926170.8980.9730.2520.6060.55699.9
2.95-3.016.20.49625800.9160.9780.2160.5410.561100
3.01-3.076.10.42125950.9190.9790.1840.460.5999.9
3.07-3.146.20.36526230.9450.9860.1580.3990.732100
3.14-3.216.10.32526050.9520.9880.1410.3550.72899.9
3.21-3.296.10.28625810.9660.9910.1240.3130.70799.9
3.29-3.386.10.25826330.9640.9910.1120.2820.813100
3.38-3.486.10.2826100.3540.7230.1280.3091.118100
3.48-3.596.10.18525870.9770.9940.080.2021.04599.9
3.59-3.726.10.1826240.9810.9950.0790.1971.141100
3.72-3.8760.16426000.9690.9920.0710.1791.50899.9
3.87-4.0460.16225830.9780.9940.0710.1771.5199.7
4.04-4.265.90.13326250.9720.9930.0580.1461.79399.6
4.26-4.525.80.1326210.9640.9910.0580.1431.90999.5
4.52-4.875.70.11625790.9810.9950.0520.1271.80599.7
4.87-5.365.20.11926070.9720.9930.0550.1312.52399.1
5.36-6.145.50.12825700.9610.990.0570.1412.89498
6.14-7.736.50.11226440.9720.9930.0470.1213.101100
7.73-506.40.16526850.9040.9750.070.1813.552100

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→49.39 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.886 / SU B: 16.235 / SU ML: 0.304 / Cross valid method: THROUGHOUT / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2618 2576 4.9 %RANDOM
Rwork0.21353 ---
obs0.21591 49543 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.93 Å2
Baniso -1Baniso -2Baniso -3
1-7.32 Å2-0 Å2-0.2 Å2
2---1.58 Å20 Å2
3----4.51 Å2
Refinement stepCycle: 1 / Resolution: 2.85→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13000 0 88 0 13088
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01213404
X-RAY DIFFRACTIONr_bond_other_d0.0020.01612142
X-RAY DIFFRACTIONr_angle_refined_deg1.411.6418108
X-RAY DIFFRACTIONr_angle_other_deg0.4651.55828291
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.31751624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.8311092
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.36102304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0660.21944
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215204
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022728
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.0645.5186520
X-RAY DIFFRACTIONr_mcbond_other5.0615.5186520
X-RAY DIFFRACTIONr_mcangle_it7.5668.2528136
X-RAY DIFFRACTIONr_mcangle_other7.5658.2538137
X-RAY DIFFRACTIONr_scbond_it5.3775.9236884
X-RAY DIFFRACTIONr_scbond_other5.3755.9246881
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.0888.7239973
X-RAY DIFFRACTIONr_long_range_B_refined10.44869.42814924
X-RAY DIFFRACTIONr_long_range_B_other10.44869.42814925
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.85→2.916 Å
RfactorNum. reflection% reflection
Rfree0.331 177 -
Rwork0.294 3527 -
obs--95.98 %

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