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- PDB-6at7: Phenylalanine Ammonia-Lyase (PAL) from Sorghum bicolor -

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Basic information

Entry
Database: PDB / ID: 6at7
TitlePhenylalanine Ammonia-Lyase (PAL) from Sorghum bicolor
ComponentsPhenylalanine ammonia-lyase
KeywordsLYASE / SbPAL / monocots
Function / homology
Function and homology information


ammonia-lyase activity / phenylalanine ammonia-lyase / cinnamic acid biosynthetic process / phenylalanine ammonia-lyase activity / L-phenylalanine catabolic process / cytoplasm
Similarity search - Function
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) ...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
AMMONIUM ION / Phenylalanine ammonia-lyase
Similarity search - Component
Biological speciesSorghum bicolor (sorghum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.493 Å
AuthorsJun, S.Y. / Kang, C.
CitationJournal: Plant Physiol. / Year: 2018
Title: Biochemical and Structural Analysis of Substrate Specificity of a Phenylalanine Ammonia-Lyase.
Authors: Jun, S.Y. / Sattler, S.A. / Cortez, G.S. / Vermerris, W. / Sattler, S.E. / Kang, C.
History
DepositionAug 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
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 / citation / citation_author / database_2 / pdbx_validate_close_contact / 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 / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_close_contact.auth_atom_id_1 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,3464
Polymers151,3102
Non-polymers362
Water8,035446
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9570 Å2
ΔGint-43 kcal/mol
Surface area50030 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)302,6938
Polymers302,6214
Non-polymers724
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_565-x,-y+1,z1
Buried area36620 Å2
ΔGint-153 kcal/mol
Surface area82570 Å2
MethodPISA
3
A: Phenylalanine ammonia-lyase
hetero molecules

B: Phenylalanine ammonia-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,3464
Polymers151,3102
Non-polymers362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_565-x,-y+1,z1
Buried area7610 Å2
ΔGint-26 kcal/mol
Surface area51980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.304, 126.304, 337.477
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Phenylalanine ammonia-lyase


Mass: 75655.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sorghum bicolor (sorghum) / Gene: SORBI_004G220300 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C5XXT8, phenylalanine ammonia-lyase
#2: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / 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: 2.22 Å3/Da / Density % sol: 44.66 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 200 mM Ammonium formate pH 6.6, 20 % w/v polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 1, 2017
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: 2.493→44.655 Å / Num. obs: 49311 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC1/2: 0.854 / Rmerge(I) obs: 0.104 / Net I/σ(I): 13.65

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.493→44.655 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2018 2000 4.17 %
Rwork0.1598 --
obs0.1616 47930 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.493→44.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10183 0 2 446 10631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310348
X-RAY DIFFRACTIONf_angle_d0.614046
X-RAY DIFFRACTIONf_dihedral_angle_d15.8236270
X-RAY DIFFRACTIONf_chiral_restr0.041651
X-RAY DIFFRACTIONf_plane_restr0.0041834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4933-2.55560.27561380.18093166X-RAY DIFFRACTION98
2.5556-2.62470.21111410.17333232X-RAY DIFFRACTION100
2.6247-2.70190.22331400.17373239X-RAY DIFFRACTION100
2.7019-2.78910.25011410.17373232X-RAY DIFFRACTION100
2.7891-2.88880.23281420.17923251X-RAY DIFFRACTION100
2.8888-3.00440.24181420.18233263X-RAY DIFFRACTION100
3.0044-3.14110.19841420.18173246X-RAY DIFFRACTION100
3.1411-3.30670.26241420.17863263X-RAY DIFFRACTION100
3.3067-3.51380.21071410.17333265X-RAY DIFFRACTION100
3.5138-3.7850.22081430.16113274X-RAY DIFFRACTION100
3.785-4.16560.19151440.14053308X-RAY DIFFRACTION100
4.1656-4.76780.16841440.12833312X-RAY DIFFRACTION100
4.7678-6.00460.17551460.15133356X-RAY DIFFRACTION100
6.0046-44.66230.1591540.15123523X-RAY DIFFRACTION100

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