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- PDB-4bab: Redesign of a Phenylalanine Aminomutase into a beta-Phenylalanine... -

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Basic information

Entry
Database: PDB / ID: 4bab
TitleRedesign of a Phenylalanine Aminomutase into a beta-Phenylalanine Ammonia Lyase
ComponentsPHENYLALANINE AMINOMUTASE
KeywordsLYASE / MIO
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 / alkaloid biosynthetic process / phenylalanine ammonia-lyase activity / 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 / Enzyme I; Chain A, domain 2 / Fumarase/aspartase (N-terminal 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 / 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
Phenylalanine aminomutase (L-beta-phenylalanine forming)
Similarity search - Component
Biological speciesTAXUS WALLICHIANA VAR. CHINENSIS (Chinese yew)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsBartsch, S. / Wybenga, G.G. / Jansen, M. / Heberling, M.M. / Wu, B. / Dijkstra, B.W. / Janssen, D.B.
CitationJournal: To be Published
Title: Redesign of a Phenylalanine Aminomutase Into a Phenylalanine Ammonia Lyase
Authors: Bartsch, S. / Wybenga, G.G. / Jansen, M. / Heberling, M.M. / Wu, B. / Dijkstra, B.W. / Janssen, D.B.
History
DepositionSep 12, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 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
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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_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 / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHENYLALANINE AMINOMUTASE
B: PHENYLALANINE AMINOMUTASE
C: PHENYLALANINE AMINOMUTASE
D: PHENYLALANINE AMINOMUTASE


Theoretical massNumber of molelcules
Total (without water)310,2154
Polymers310,2154
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31070 Å2
ΔGint-166.5 kcal/mol
Surface area73450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.136, 132.095, 110.035
Angle α, β, γ (deg.)90.00, 95.52, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9743, 0.2214, -0.04114), (0.2232, 0.9255, -0.3061), (-0.02969, -0.3074, -0.951)-47.09, -2.759, -51.04
2given(0.1517, 0.02098, 0.9882), (0.01872, -0.9997, 0.01835), (0.9883, 0.01571, -0.152)11.07, 46.2, -13.7
3given(-0.1854, -0.2476, -0.951), (-0.2478, -0.9247, 0.289), (-0.9509, 0.2892, 0.1101)-46.79, 47, -52.45

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Components

#1: Protein
PHENYLALANINE AMINOMUTASE


Mass: 77553.633 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TAXUS WALLICHIANA VAR. CHINENSIS (Chinese yew)
Production host: ESCHERICHIA COLI K-12 (bacteria) / Strain (production host): TOP10 / References: UniProt: Q68G84
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSEQUENCE INCLUDES AN N-TERMINAL LINKER OF 20 AMINO ACIDS AND INCLUDES AN R92S AND R93S MUTATION

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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: 2.19 Å3/Da / Density % sol: 43.94 % / Description: NONE
Crystal growDetails: 0.2 M NA FORMATE, 20 % W/V PEG 3350, 2 MM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9203
DetectorDate: Dec 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9203 Å / Relative weight: 1
ReflectionResolution: 2.56→49.52 Å / Num. obs: 83419 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 53.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.7
Reflection shellResolution: 2.56→2.7 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.1 / % possible all: 89.8

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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: 2.56→109.52 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.915 / SU B: 11.377 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R: 1.626 / ESU R Free: 0.326 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25103 4212 5.1 %RANDOM
Rwork0.21403 ---
obs0.2159 79180 97.04 %-
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: 54.459 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å20 Å20.55 Å2
2--0.49 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 2.56→109.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19180 0 0 36 19216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0219515
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9531.98426469
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.50952435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99924.046833
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.24153395
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.48515136
X-RAY DIFFRACTIONr_chiral_restr0.0610.23134
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02114432
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: 2.564→2.631 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 263 -
Rwork0.281 4775 -
obs--80.63 %

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