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- PDB-2nyn: Crystal structure of phenylalanine ammonia-lyase from Anabaena va... -

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Basic information

Entry
Database: PDB / ID: 2nyn
TitleCrystal structure of phenylalanine ammonia-lyase from Anabaena variabilis
ComponentsPhenylalanine/histidine ammonia-lyase
KeywordsLYASE / Methylidene imidazolone prosthetic group
Function / homology
Function and homology information


phenylalanine ammonia-lyase / cinnamic acid biosynthetic process / phenylalanine ammonia-lyase activity / phenylpropanoid biosynthetic process / aromatic amino acid metabolic process / L-phenylalanine catabolic process / protein homotetramerization / cytoplasm
Similarity search - Function
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 ...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 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Phenylalanine ammonia-lyase
Similarity search - Component
Biological speciesAnabaena variabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLouie, G.V. / Moffitt, M.C. / Bowman, M.E. / Pence, J. / Noel, J.P. / Moore, B.S.
CitationJournal: Biochemistry / Year: 2007
Title: Discovery of Two Cyanobacterial Phenylalanine Ammonia Lyases: Kinetic and Structural Characterization.
Authors: Moffitt, M.C. / Louie, G.V. / Bowman, M.E. / Pence, J. / Noel, J.P. / Moore, B.S.
History
DepositionNov 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / 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 / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999Sequence Residue MDO is autocatalytically formed by internal tripeptide segment Ala167-Ser168-Gly169

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phenylalanine/histidine ammonia-lyase
B: Phenylalanine/histidine ammonia-lyase
C: Phenylalanine/histidine ammonia-lyase
D: Phenylalanine/histidine ammonia-lyase


Theoretical massNumber of molelcules
Total (without water)247,0524
Polymers247,0524
Non-polymers00
Water9,746541
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26970 Å2
ΔGint-156 kcal/mol
Surface area58870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.193, 88.515, 90.058
Angle α, β, γ (deg.)103.52, 97.82, 116.24
Int Tables number1
Space group name H-MP1
DetailsBiological unit: homotetramer. The 222 symmetric homotetramer is the contents of the asymmetric unit.

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Components

#1: Protein
Phenylalanine/histidine ammonia-lyase


Mass: 61762.941 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena variabilis (bacteria) / Strain: 29413 / Plasmid: pHIS8 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q3M5Z3, histidine ammonia-lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 541 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M MOPSO, 7% (w/v) polyethylene glycol 8000, 0.2 M magnesium chloride, 10 mM cinnamic acid, 2 mM dithiothreitol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 1, 2005
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. obs: 159839 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.15 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 7.94
Reflection shellResolution: 1.9→1.99 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 3.2 / Num. unique all: 20762 / % possible all: 88.4

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Processing

Software
NameVersionClassification
MOLREPphasing
CNS1.1refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1W27

1w27


Resolution: 1.9→100 Å / Isotropic thermal model: Isotropic / Cross valid method: Random / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.242 7620 Random
Rwork0.223 --
obs-151571 -
Displacement parametersBiso mean: 30.7 Å2
Refinement stepCycle: LAST / Resolution: 1.9→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15720 0 0 541 16261
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.16
X-RAY DIFFRACTIONc_mcbond_it1.9
X-RAY DIFFRACTIONc_mcangle_it2.59
X-RAY DIFFRACTIONc_scbond_it2.69
LS refinement shellResolution: 1.9→1.99 Å
RfactorNum. reflection
Rfree0.334 897
Rwork0.295 -
obs-16736

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