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- PDB-4v2q: Ironing out their differences: Dissecting the structural determin... -

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Basic information

Entry
Database: PDB / ID: 4v2q
TitleIroning out their differences: Dissecting the structural determinants of a phenylalanine aminomutase and ammonia lyase
ComponentsPHENYLALANINE AMMONIA-LYASE
KeywordsLYASE
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: 1.95 Å
AuthorsHeberling, M. / Masman, M. / Bartsch, S. / Wybenga, G.G. / Dijkstra, B.W. / Marrink, S. / Janssen, D.
CitationJournal: Acs Chem.Biol. / Year: 2015
Title: Ironing Out Their Differences: Dissecting the Structural Determinants of a Phenylalanine Aminomutase and Ammonia Lyase.
Authors: Heberling, M.M. / Masman, M.F. / Bartsch, S. / Wybenga, G.G. / Dijkstra, B.W. / Marrink, S.J. / Janssen, D.B.
History
DepositionOct 14, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Apr 29, 2015Group: Database references
Revision 1.3Oct 23, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_special_symmetry ...pdbx_database_status / pdbx_struct_special_symmetry / 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 / 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 / _pdbx_validate_polymer_linkage.auth_atom_id_1 / _pdbx_validate_polymer_linkage.auth_atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Jan 10, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHENYLALANINE AMMONIA-LYASE
B: PHENYLALANINE AMMONIA-LYASE


Theoretical massNumber of molelcules
Total (without water)154,9912
Polymers154,9912
Non-polymers00
Water5,026279
1
A: PHENYLALANINE AMMONIA-LYASE
B: PHENYLALANINE AMMONIA-LYASE

A: PHENYLALANINE AMMONIA-LYASE
B: PHENYLALANINE AMMONIA-LYASE


Theoretical massNumber of molelcules
Total (without water)309,9824
Polymers309,9824
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area30540 Å2
ΔGint-166 kcal/mol
Surface area73460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.531, 76.173, 120.446
Angle α, β, γ (deg.)90.00, 120.42, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2106-

HOH

21B-2081-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: generate
Matrix: (-0.1272, 0.002845, 0.9919), (-0.001886, -1, 0.002627), (0.9919, -0.001536, 0.1273)
Vector: -85.68, -86.78, 75.61)

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Components

#1: Protein PHENYLALANINE AMMONIA-LYASE / / PHENYLALANINE AMINOMUTASE


Mass: 77495.484 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsL97G C89T MUTANT

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.84 % / Description: NONE

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.99989
DetectorDate: Feb 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99989 Å / Relative weight: 1
ReflectionResolution: 1.95→47.38 Å / Num. obs: 103115 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.1
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9

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Processing

SoftwareName: REFMAC / Version: 5.6.0117 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YII

2yii


Resolution: 1.95→103.87 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.371 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21607 5159 5 %RANDOM
Rwork0.18968 ---
obs0.19101 97956 99.74 %-
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: 29.043 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å21.89 Å2
2--1.32 Å20 Å2
3---0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.95→103.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9599 0 0 279 9878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.029758
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2061.98313239
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.29251216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34824.105419
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.612151692
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8551568
X-RAY DIFFRACTIONr_chiral_restr0.0810.21571
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217216
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: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 369 -
Rwork0.249 7054 -
obs--99.88 %

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