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- PDB-3nz4: Crystal Structure of a Taxus Phenylalanine Aminomutase -

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Basic information

Entry
Database: PDB / ID: 3nz4
TitleCrystal Structure of a Taxus Phenylalanine Aminomutase
ComponentsPhenylalanine ammonia-lyase
KeywordsLYASE / Aminomutase / Taxol biosynthetic pathway / MIO / phenylalanine
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
PHENYLETHYLENECARBOXYLIC ACID / Phenylalanine aminomutase (L-beta-phenylalanine forming)
Similarity search - Component
Biological speciesTaxus canadensis (Canada yew)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsFeng, L. / Geiger, J.H.
CitationJournal: Biochemistry / Year: 2011
Title: Mechanistic, mutational, and structural evaluation of a taxus phenylalanine aminomutase.
Authors: Feng, L. / Wanninayake, U. / Strom, S. / Geiger, J. / Walker, K.D.
History
DepositionJul 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,4854
Polymers153,1892
Non-polymers2962
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7680 Å2
ΔGint-33 kcal/mol
Surface area47820 Å2
MethodPISA
2
A: Phenylalanine ammonia-lyase
B: Phenylalanine ammonia-lyase
hetero molecules

A: Phenylalanine ammonia-lyase
B: Phenylalanine ammonia-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)306,9718
Polymers306,3784
Non-polymers5934
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area36190 Å2
ΔGint-170 kcal/mol
Surface area74820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.733, 76.113, 120.392
Angle α, β, γ (deg.)90.00, 120.43, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-728-

HOH

21B-806-

HOH

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Components

#1: Protein Phenylalanine ammonia-lyase /


Mass: 76594.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Taxus canadensis (Canada yew) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6GZ04, phenylalanine ammonia-lyase
#2: Chemical ChemComp-TCA / PHENYLETHYLENECARBOXYLIC ACID / Cinnamic acid


Mass: 148.159 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H8O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O

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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: 2.34 Å3/Da / Density % sol: 47.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M HEPES, pH 7.0, 1.0M LiCl, 15% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0782 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0782 Å / Relative weight: 1
ReflectionResolution: 2.38→103.81 Å / Num. all: 55249 / Num. obs: 49662 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shellResolution: 2.38→2.42 Å / % possible all: 79.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→103.81 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.926 / SU B: 17.906 / SU ML: 0.187 / Cross valid method: THROUGHOUT / σ(F): 5 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23926 5580 10.1 %RANDOM
Rwork0.18301 ---
all0.1887 55249 --
obs0.1887 49662 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.117 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å22.18 Å2
2--0.35 Å20 Å2
3---1.93 Å2
Refinement stepCycle: LAST / Resolution: 2.38→103.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10147 0 22 276 10445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02210377
X-RAY DIFFRACTIONr_angle_refined_deg1.311.98314076
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.55951306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00523.81441
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.021151801
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1371578
X-RAY DIFFRACTIONr_chiral_restr0.10.21654
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217722
X-RAY DIFFRACTIONr_mcbond_it0.4951.56542
X-RAY DIFFRACTIONr_mcangle_it0.958210550
X-RAY DIFFRACTIONr_scbond_it1.53333835
X-RAY DIFFRACTIONr_scangle_it2.5624.53526
LS refinement shellResolution: 2.38→2.442 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 369 -
Rwork0.236 3035 -
obs--81.45 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.3801-0.4158-1.09411.02870.42250.9790.0618-0.0993-0.02170.0958-0.07620.1868-0.0148-0.13280.01430.10570.0029-0.0560.09680.00450.1146-59.593642.769244.3214
20.7431-0.0623-0.30650.22360.00620.49630.0310.09680.0484-0.076-0.015-0.0114-0.04260.0453-0.0160.15250.0067-0.03790.11040.00480.1009-27.516936.705932.2176
31.1594-0.1999-0.3390.68450.19160.66960.01640.1873-0.1811-0.1155-0.0203-0.02910.05280.00960.00390.1542-0.0053-0.06260.0997-0.02770.1589-40.0155.082634.603
40.97290.1204-0.42030.37050.02420.7550.041-0.1087-0.08520.0887-0.05180.10010.0275-0.13120.01080.1164-0.011-0.04480.0860.01780.1366-57.42999.444563.0378
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 102
2X-RAY DIFFRACTION2A103 - 678
3X-RAY DIFFRACTION3B7 - 355
4X-RAY DIFFRACTION4B356 - 678

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