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Basic information

Entry
Database: PDB / ID: 4c5r
TitleStructural Investigations into the Stereochemistry and Activity of a Phenylalanine-2,3-Aminomutase from Taxus chinensis
ComponentsPHENYLALANINE AMMONIA-LYASE
KeywordsLYASE / (R)-BETA-PHENYLALANINE ANALOGUE
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: 2.14 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: Atomic model / Data collection ...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_rmsd_angle / 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 / _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 2.2Nov 13, 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)311,20310
Polymers310,2154
Non-polymers9896
Water11,548641
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37830 Å2
ΔGint-172.4 kcal/mol
Surface area69310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.395, 145.477, 99.564
Angle α, β, γ (deg.)90.00, 99.54, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.2657, -0.2196, 0.9387), (-0.2122, -0.9365, -0.2792), (0.9404, -0.2734, 0.2022)10.44, 20.45, -3.447
2given(-0.8854, 0.4645, 0.01683), (0.4646, 0.8833, 0.06326), (0.01452, 0.06383, -0.9979)-39.07, 11.65, -60.75
3given(0.1487, -0.2511, -0.9565), (-0.2521, -0.9449, 0.2088), (-0.9562, 0.2101, -0.2038)-38.84, 34.5, -55.74

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Components

#1: Protein
PHENYLALANINE AMMONIA-LYASE / PHENYLALANINE AMINOMUTASE


Mass: 77553.633 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: PEPTIDE BOND BETWEEN SER174 AND MDO 175 PEPTIDE BOND BETWEEN MDO 175 AND D178 COVALENT BOND BETWEEN THE CB2 ATOM OF MDO AND THE BETA-AMINO GROUP OF THE R-BETA-PHE SUBSTRATE ANALOGUE
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 641 / 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: 2.29 Å3/Da / Density % sol: 46.25 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.14→49.09 Å / Num. obs: 151434 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.9
Reflection shellResolution: 2.14→2.26 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3 / % possible all: 97.5

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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: 2.14→49.09 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.497 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20989 7602 5 %RANDOM
Rwork0.17204 ---
obs0.17394 143786 99.4 %-
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: 25.029 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å20.99 Å2
2---0.02 Å20 Å2
3---0.85 Å2
Refinement stepCycle: LAST / Resolution: 2.14→49.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19796 0 68 641 20505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0220208
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2541.98627401
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.45452523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.68223.855856
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.416153484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.73615148
X-RAY DIFFRACTIONr_chiral_restr0.0880.23242
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02114952
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: 2.145→2.201 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 531 -
Rwork0.214 10032 -
obs--95.33 %

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