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- PDB-1w27: Phenylalanine ammonia-lyase (PAL) from Petroselinum crispum -

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Basic information

Entry
Database: PDB / ID: 1w27
TitlePhenylalanine ammonia-lyase (PAL) from Petroselinum crispum
ComponentsPHENYLALANINE AMMONIA-LYASE 1
KeywordsLYASE / PHENYLPROPANOID METABOLISM / MIO
Function / homology
Function and homology information


phenylalanine ammonia-lyase / cinnamic acid biosynthetic process / phenylalanine ammonia-lyase activity / L-phenylalanine catabolic process / amino acid binding / protein-containing complex / cytoplasm
Similarity search - Function
Phenylalanine ammonia-lyase 1; domain 3 / Phenylalanine ammonia-lyase / Phenylalanine ammonia-lyase, shielding domain superfamily / Phenylalanine/histidine ammonia-lyases, active site / Phenylalanine and histidine ammonia-lyases signature. / Aromatic amino acid lyase / Aromatic amino acid lyase / Enzyme I; Chain A, domain 2 / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) ...Phenylalanine ammonia-lyase 1; domain 3 / Phenylalanine ammonia-lyase / Phenylalanine ammonia-lyase, shielding domain superfamily / Phenylalanine/histidine ammonia-lyases, active site / Phenylalanine and histidine ammonia-lyases signature. / Aromatic amino acid lyase / Aromatic amino acid lyase / Enzyme I; Chain A, domain 2 / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarase/histidase, N-terminal / L-Aspartase-like / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Phenylalanine ammonia-lyase 1
Similarity search - Component
Biological speciesPETROSELINUM CRISPUM (parsley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsRitter, H. / Schulz, G.E.
CitationJournal: Plant Cell / Year: 2004
Title: Structural Basis for the Entrance Into the Phenylpropanoid Metabolism Catalyzed by Phenylalanine Ammonia-Lyase
Authors: Ritter, H. / Schulz, G.E.
History
DepositionJun 29, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHENYLALANINE AMMONIA-LYASE 1
B: PHENYLALANINE AMMONIA-LYASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,0664
Polymers155,7572
Non-polymers3092
Water19,2941071
1
A: PHENYLALANINE AMMONIA-LYASE 1
B: PHENYLALANINE AMMONIA-LYASE 1
hetero molecules

A: PHENYLALANINE AMMONIA-LYASE 1
B: PHENYLALANINE AMMONIA-LYASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,1328
Polymers311,5154
Non-polymers6174
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area36910 Å2
ΔGint-179.25 kcal/mol
Surface area86940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.960, 160.810, 141.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (0.757, 0.653), (-1), (0.653, -0.757) / Vector: -23.064, 74.738, 62.081)

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Components

#1: Protein PHENYLALANINE AMMONIA-LYASE 1 /


Mass: 77878.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PETROSELINUM CRISPUM (parsley) / Description: SYNTHETIC GENE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P24481, EC: 4.3.1.5
#2: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1071 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENZYME OF PLANT METABOLISM CATALYZING THE FIRST REACTION IN THE BIOSYNTHESIS FROM L-PHENYLALANINE. ...ENZYME OF PLANT METABOLISM CATALYZING THE FIRST REACTION IN THE BIOSYNTHESIS FROM L-PHENYLALANINE. CONTAINS AN ACTIVE SITE 4-METHYLIDENE-IMIDAZOLE-5-ONE (MIO), WHICH IS FORMED AUTOCATALYTICALLY BY CYCLIZATION AND DEHYDRATION OF RESIDUES ALA-SER-GLY.

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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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growpH: 7.5 / Details: 8% PEG-6000, 40 MM MGCL2, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.9798,0.9800,0.9824
DetectorDate: Nov 15, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97981
20.981
30.98241
ReflectionResolution: 1.7→50 Å / Num. obs: 156788 / % possible obs: 96.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 21.4
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 4.5 / % possible all: 88.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
MLPHAREphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.667 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.199 7349 5 %RANDOM
Rwork0.166 ---
obs0.168 139351 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 21.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0.09 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10576 0 16 1071 11663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02110780
X-RAY DIFFRACTIONr_bond_other_d0.0020.029896
X-RAY DIFFRACTIONr_angle_refined_deg1.3661.97114584
X-RAY DIFFRACTIONr_angle_other_deg0.876323098
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.93951374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0830.21668
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211962
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022028
X-RAY DIFFRACTIONr_nbd_refined0.2420.22776
X-RAY DIFFRACTIONr_nbd_other0.2340.212270
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.26257
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2825
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2730.256
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2880.2245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.259
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7671.56850
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.41211016
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.19433930
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6054.53568
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
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.222 497
Rwork0.193 10140

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