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- PDB-5hsj: Structure of tyrosine decarboxylase complex with PLP at 1.9 Angst... -

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Basic information

Entry
Database: PDB / ID: 5hsj
TitleStructure of tyrosine decarboxylase complex with PLP at 1.9 Angstroms resolution
ComponentsPutative decarboxylase
KeywordsLYASE / tyrosine decarboxylase / PLP
Function / homology
Function and homology information


L-dopa decarboxylase activity / tyrosine decarboxylase / tyrosine decarboxylase activity / carboxylic acid metabolic process / pyridoxal phosphate binding
Similarity search - Function
Tyrosine decarboxylase, bacteria / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / L-tyrosine decarboxylase
Similarity search - Component
Biological speciesLactobacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNi, Y. / Zhou, J. / Zhu, H. / Zhang, K.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China21276112 China
National Natural Science Foundation of China21506073 China
Natural Science Foundation of Jiangsu ProvinceBK20150003 China
Science and Technology Commission of Shanghai Municipality15JC1400403 China
CitationJournal: Sci Rep / Year: 2016
Title: Crystal structure of tyrosine decarboxylase and identification of key residues involved in conformational swing and substrate binding
Authors: Zhu, H.X. / Xu, G.C. / Zhang, K. / Kong, X.D. / Han, R.Z. / Zhou, J.H. / Ni, Y.
History
DepositionJan 25, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative decarboxylase
B: Putative decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,8184
Polymers143,3242
Non-polymers4942
Water10,215567
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14440 Å2
ΔGint-89.5 kcal/mol
Surface area40680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.869, 126.830, 82.877
Angle α, β, γ (deg.)90.00, 109.73, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A-99999 - 99999
2111B-99999 - 99999

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.935849, -0.333974, -0.112462), (-0.344958, 0.802937, 0.486102), (-0.072046, 0.493713, -0.866635)70.17628, -36.4385, 182.88261

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Components

#1: Protein Putative decarboxylase / L-Tyrosine decarboxylase / Tyrosine decarboxylase


Mass: 71661.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus brevis (bacteria) / Gene: tdc, N624_0219 / Production host: Escherichia coli (E. coli) / References: UniProt: J7GQ11, tyrosine decarboxylase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 567 / Source method: isolated from a natural source / Formula: H2O

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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: 2.17 Å3/Da / Density % sol: 43.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7
Details: PEG 4000, sodium cacodylate trihydrate, magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97908 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 94427 / % possible obs: 99.7 % / Redundancy: 5.2 % / Net I/σ(I): 10
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.2 % / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
PHENIXv1.9phasing
PHENIXv1.9model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HSI

5hsi


Resolution: 1.9→49.26 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.338 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21243 4731 5 %RANDOM
Rwork0.1715 ---
obs0.17355 89685 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.63 Å2
Baniso -1Baniso -2Baniso -3
1-2.69 Å2-0 Å2-1.77 Å2
2---1.2 Å2-0 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.9→49.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9539 0 31 567 10137
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0199794
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1291.95613267
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20151194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3724.571466
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.769151656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2561544
X-RAY DIFFRACTIONr_chiral_restr0.150.21403
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0217502
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCSNumber: 4726 / Type: tight thermal / Rms dev position: 8.91 Å / Weight position: 0.5
LS refinement shellResolution: 1.898→1.947 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 345 -
Rwork0.257 6496 -
obs--97.71 %

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