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Basic information

Entry
Database: PDB / ID: 4c5s
TitleStructural Investigations into the Stereochemistry and Activity of a Phenylalanine-2,3-Aminomutase from Taxus chinensis
ComponentsPHENYLALANINE AMMONIA-LYASE
KeywordsLYASE / (R)-BETA-PHENYLALANINE ANALOGUE / METHYLIDENE-IMIDAZOLE-5-ONE / Y80A
Function / homology
Function and homology information


phenylalanine aminomutase (L-beta-phenylalanine-forming) / intramolecular aminotransferase activity / paclitaxel biosynthetic process / phenylalanine ammonia-lyase / L-phenylalanine metabolic process / cinnamic acid biosynthetic process / phenylalanine ammonia-lyase activity / alkaloid biosynthetic process / L-phenylalanine catabolic process / protein homotetramerization / cytoplasm
Similarity search - Function
Phenylalanine aminomutase (L-beta-phenylalanine forming) / 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 / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) ...Phenylalanine aminomutase (L-beta-phenylalanine forming) / 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 / 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 / Enzyme I; Chain A, domain 2 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
(3S)-3-amino-2,2-difluoro-3-phenylpropanoic acid / Phenylalanine aminomutase (L-beta-phenylalanine forming)
Similarity search - Component
Biological speciesTAXUS WALLICHIANA VAR. CHINENSIS (Chinese yew)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsWybenga, G.G. / Szymanski, W. / Wu, B. / Feringa, B.L. / Janssen, D.B. / Dijkstra, B.W.
CitationJournal: Biochemistry / Year: 2014
Title: Structural Investigations Into the Stereochemistry and Activity of a Phenylalanine-2,3-Aminomutase from Taxus Chinensis.
Authors: Wybenga, G.G. / Szymanski, W. / Wu, B. / Feringa, B.L. / Janssen, D.B. / Dijkstra, B.W.
History
DepositionSep 16, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2Jun 4, 2014Group: Database references
Revision 1.3Oct 23, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_polymer_linkage / 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_validate_polymer_linkage.auth_atom_id_1 / _pdbx_validate_polymer_linkage.auth_atom_id_2 / _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
Revision 2.1Dec 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHENYLALANINE AMMONIA-LYASE
B: PHENYLALANINE AMMONIA-LYASE
C: PHENYLALANINE AMMONIA-LYASE
D: PHENYLALANINE AMMONIA-LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)310,6518
Polymers309,8464
Non-polymers8054
Water15,583865
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36640 Å2
ΔGint-183.3 kcal/mol
Surface area70830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.751, 146.185, 100.395
Angle α, β, γ (deg.)90.00, 99.31, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.2666, -0.2203, 0.9383), (-0.2188, -0.9343, -0.2815), (0.9387, -0.2803, 0.2009)11.5, 28.12, -2.358
2given(0.1513, -0.2453, -0.9576), (-0.2481, -0.9471, 0.2035), (-0.9568, 0.2068, -0.2042)-38.33, 42.52, -57.1
3given(0.1513, -0.2453, -0.9576), (-0.2481, -0.9471, 0.2035), (-0.9568, 0.2068, -0.2042)-38.33, 42.52, -57.1

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Components

#1: Protein
PHENYLALANINE AMMONIA-LYASE / PHENYLALANINE AMINOMUTASE


Mass: 77461.539 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TAXUS WALLICHIANA VAR. CHINENSIS (Chinese yew)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q68G84, phenylalanine ammonia-lyase
#2: Chemical
ChemComp-BQ7 / (3S)-3-amino-2,2-difluoro-3-phenylpropanoic acid


Mass: 201.170 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H9F2NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 865 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.24 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.85→48.73 Å / Num. obs: 241051 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.3
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YII

2yii


Resolution: 1.85→99.07 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.558 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20528 12073 5 %RANDOM
Rwork0.17835 ---
obs0.1797 228937 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.456 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20.75 Å2
2--0.57 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.85→99.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19876 0 56 865 20797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0220271
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2971.98527503
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.47452538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1623.914861
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.665153504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1915148
X-RAY DIFFRACTIONr_chiral_restr0.0860.23254
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02115020
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
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 883 -
Rwork0.251 16645 -
obs--100 %

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