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- PDB-8jik: Alanine decarboxylase -

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Basic information

Entry
Database: PDB / ID: 8jik
TitleAlanine decarboxylase
ComponentsSerine decarboxylase
KeywordsLYASE / PLP / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


carboxylic acid metabolic process / carboxy-lyase activity / pyridoxal phosphate binding / metal ion binding
Similarity search - Function
: / 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
ETHANAMINE / Serine decarboxylase
Similarity search - Component
Biological speciesCamellia sinensis (black tea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGong, W. / Wang, H.
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 26, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2024Provider: repository / Type: Initial release
Revision 2.0Dec 4, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / citation / citation_author / entity / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_validate_close_contact / pdbx_validate_torsion / struct_asym / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _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 / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _pdbx_entry_details.has_protein_modification / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_torsion.auth_comp_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1044
Polymers47,9531
Non-polymers1513
Water1,08160
1
A: Serine decarboxylase
hetero molecules

A: Serine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,2088
Polymers95,9072
Non-polymers3016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area10250 Å2
ΔGint-63 kcal/mol
Surface area28970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.996, 163.996, 50.209
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Serine decarboxylase / Alanine decarboxylase


Mass: 47953.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camellia sinensis (black tea) / Gene: TEA_005062 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4S4ESS1
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NEH / ETHANAMINE


Mass: 45.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H7N
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 4.19 Å3/Da / Density % sol: 70.61 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 2.8 M Sodium acetate trihydrate, pH 7.0

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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: Jun 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 24010 / % possible obs: 99.6 % / Redundancy: 13 % / Rmerge(I) obs: 0.156 / Net I/σ(I): 3.8
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.562 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→17.62 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / SU B: 7.583 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1186 4.9 %RANDOM
Rwork0.172 ---
obs0.174 22813 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å20 Å2
2--0.18 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 2.6→17.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3258 0 20 60 3338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123372
X-RAY DIFFRACTIONr_bond_other_d0.0020.0163058
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.6374555
X-RAY DIFFRACTIONr_angle_other_deg0.5521.5547124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3495410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.4051021
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.52710571
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0780.2487
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023823
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02694
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_it4.2534.61642
X-RAY DIFFRACTIONr_mcbond_other4.2524.5991643
X-RAY DIFFRACTIONr_mcangle_it6.3046.8982047
X-RAY DIFFRACTIONr_mcangle_other6.3036.8972048
X-RAY DIFFRACTIONr_scbond_it4.5674.9291730
X-RAY DIFFRACTIONr_scbond_other4.5664.9281731
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7827.2292508
X-RAY DIFFRACTIONr_long_range_B_refined8.79756.8833727
X-RAY DIFFRACTIONr_long_range_B_other8.79356.6443724
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.66 Å
RfactorNum. reflection% reflection
Rfree0.324 107 -
Rwork0.259 1580 -
obs--99.24 %

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