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- PDB-4c6g: Structural Investigations into the Stereochemistry and Activity o... -

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Basic information

Entry
Database: PDB / ID: 4c6g
TitleStructural Investigations into the Stereochemistry and Activity of a Phenylalanine-2,3-Aminomutase from Taxus chinensis
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 / 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
Phenylalanine aminomutase (L-beta-phenylalanine forming)
Similarity search - Component
Biological speciesTAXUS WALLICHIANA VAR. CHINENSIS (Chinese yew)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 18, 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 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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


Theoretical massNumber of molelcules
Total (without water)310,1874
Polymers310,1874
Non-polymers00
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31350 Å2
ΔGint-174 kcal/mol
Surface area72110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.960, 146.572, 99.334
Angle α, β, γ (deg.)90.00, 100.02, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.1346, -0.2426, 0.9607), (-0.2404, -0.9326, -0.2692), (0.9613, -0.2672, 0.06721)9.096, 12.14, -5.148
2given(-1, -9.9E-5, 0.000864), (0.000324, 0.8794, 0.476), (-0.000807, 0.476, -0.8794)52.25, -10.25, 40.13
3given(0.1336, 0.2434, -0.9607), (0.2439, -0.9476, -0.2062), (-0.9605, -0.2068, -0.186)43.19, -1.94, 50.55

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Components

#1: Protein
PHENYLALANINE AMMONIA-LYASE / PHENYLALANINE AMINOMUTASE


Mass: 77546.641 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, EC: 5.4.3.-, phenylalanine ammonia-lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O

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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: 46.22 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97934
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.1→48.91 Å / Num. obs: 161887 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 29.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.2
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.9 / % possible all: 99.5

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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: 2.1→48.73 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.203 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24101 8119 5 %RANDOM
Rwork0.20084 ---
obs0.20286 153649 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: 46.036 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20 Å22.25 Å2
2--0.64 Å20 Å2
3----1.26 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19367 0 0 220 19587
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01919700
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.281.98126733
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.50352477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.42923.99832
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.608153415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.07115136
X-RAY DIFFRACTIONr_chiral_restr0.0870.23172
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02114573
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: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 603 -
Rwork0.263 11186 -
obs--99.65 %

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