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- PDB-6f6t: Phenylalanine ammonia-lyase (PAL) from Petroselinum crispum compl... -

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Basic information

Entry
Database: PDB / ID: 6f6t
TitlePhenylalanine ammonia-lyase (PAL) from Petroselinum crispum complexed with S-APPA
ComponentsPhenylalanine ammonia-lyase 1
KeywordsLYASE / Inhibitor / Complex / Phenylalanine ammonia-lyase
Function / homology
Function and homology information


phenylalanine ammonia-lyase / cinnamic acid biosynthetic process / phenylalanine ammonia-lyase activity / L-phenylalanine catabolic process / amino acid binding / protein-containing complex / 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
(S)-(1-amino-2phenylallyl)phosphonic acid / Phenylalanine ammonia-lyase 1
Similarity search - Component
Biological speciesPetroselinum crispum (parsley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89995964358 Å
AuthorsBata, Z. / Leveles, I. / Vertessy, G.B. / Poppe, L.
Funding support Hungary, Romania, 9items
OrganizationGrant numberCountry
National Research Development and Innovation OfficeNKFIH K119493 Hungary
National Research Development and Innovation OfficeNKFIH K109486 Hungary
National Research Development and Innovation OfficeNVKP-16-1-2016-0020 Hungary
National Research Development and Innovation OfficeVEKOP-2.3.2-16-2017-00013 Hungary
National Research Development and Innovation OfficeICGEB CRP/HUN14-01 Hungary
National Research Development and Innovation OfficeUNKP-2017-3-058 Hungary
EU COSTAction CM1303 SysBiocat Hungary
Hungarian OTKA FoundationNN-103242 Hungary
Romanian Ministry for European FundsNEMSyB ID P37273 Cod MySMIS 103413 Romania
Citation
Journal: Acs Catalysis / Year: 2021
Title: Substrate Tunnel Engineering Aided by X-ray Crystallography and Functional Dynamics Swaps the Function of MIO-Enzymes
Authors: Bata, Z. / Molnar, Z. / Madaras, E. / Molnar, B. / Santa-Bell, E. / Varga, A. / Leveles, I. / Qian, R. / Hammerschmidt, F. / Paizs, C. / Vertessy, B.G. / Poppe, L.
#1: Journal: Adv. Synth. Catal. / Year: 2017
Title: A Methylidene Group in the Phosphonic Acid Analogue of Phenylalanine Reverses the Enantiopreference of Binding to Phenylalanine Ammonia-Lyases.
Authors: Bata, Z. / Qian, R. / Roller, A. / Horak, J. / Bencze, L.C. / Paizs, C. / Hammerschmidt, F. / Vertessy, B.G. / Poppe, L.
#2: Journal: STUDIA UBB CHEMIA, / Year: 2016
Title: EXPRESSION AND PURIFICATION OF RECOMBINANT PHENYLALANINE AMMONIA-LYASE FROM PETROSELINUM CRISPUM
Authors: Bata, Z.
History
DepositionDec 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / struct_conn
Item: _audit_author.identifier_ORCID / _citation.country ..._audit_author.identifier_ORCID / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2Apr 14, 2021Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...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_peptide_omega / 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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phenylalanine ammonia-lyase 1
B: Phenylalanine ammonia-lyase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,1204
Polymers155,6932
Non-polymers4262
Water10,431579
1
A: Phenylalanine ammonia-lyase 1
B: Phenylalanine ammonia-lyase 1
hetero molecules

A: Phenylalanine ammonia-lyase 1
B: Phenylalanine ammonia-lyase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,2398
Polymers311,3864
Non-polymers8534
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
Buried area37050 Å2
ΔGint-168 kcal/mol
Surface area79740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.740, 161.100, 141.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-1137-

HOH

21B-1172-

HOH

31B-1184-

HOH

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Components

#1: Protein Phenylalanine ammonia-lyase 1


Mass: 77846.602 Da / Num. of mol.: 2 / Mutation: A202X, S203X, G204X, C704S, C716S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Petroselinum crispum (parsley) / Gene: PAL1 / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta / References: UniProt: P24481, phenylalanine ammonia-lyase
#2: Chemical ChemComp-CV2 / (S)-(1-amino-2phenylallyl)phosphonic acid


Mass: 213.170 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H12NO3P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 579 / 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: 2.29 Å3/Da / Density % sol: 46.4 % / Description: Tree like plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 6000 14 W/V%, HEPES 0.15 M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2016
RadiationMonochromator: KB-mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.65→95.584 Å / Num. all: 314714 / Num. obs: 106555 / % possible obs: 99.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 25.9685078708 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.15 / Net I/σ(I): 4.48
Reflection shellResolution: 1.65→1.75 Å / CC1/2: 0.641 / Rrim(I) all: 1.189

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSVERSION Jun 1, 2017 BUILT=20170615data reduction
XDSVERSION Jun 1, 2017 BUILT=20170615data scaling
PHENIX1.11.1_2575phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W27

1w27


Resolution: 1.89995964358→95.5824868269 Å / SU ML: 0.312182771342 / Cross valid method: FREE R-VALUE / σ(F): 1.33900178422 / Phase error: 26.0441066425
RfactorNum. reflection% reflectionSelection details
Rfree0.238743223725 5353 5.02751845521 %Take from 1w27.cif
Rwork0.191938851723 ---
obs0.194251206443 106474 99.8565091393 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 28.7481309341 Å2
Refinement stepCycle: LAST / Resolution: 1.89995964358→95.5824868269 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10280 0 28 579 10887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0070062340006710554
X-RAY DIFFRACTIONf_angle_d0.92252977306314308
X-RAY DIFFRACTIONf_chiral_restr0.04954131889841643
X-RAY DIFFRACTIONf_plane_restr0.005279096239461860
X-RAY DIFFRACTIONf_dihedral_angle_d14.34541541286418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.3947782293891790.3641748387743321X-RAY DIFFRACTION99.5166334945
1.9216-1.94420.393215819261840.34438366583338X-RAY DIFFRACTION99.4634284101
1.9442-1.96790.3679929923041740.3388323639383338X-RAY DIFFRACTION99.9430848036
1.9679-1.99280.368474805561860.324146896413339X-RAY DIFFRACTION99.9716392513
1.9928-2.0190.3645159476361780.3171838463753315X-RAY DIFFRACTION99.914187643
2.019-2.04670.3540258939321740.295965179223369X-RAY DIFFRACTION99.8872286439
2.0467-2.07590.3303301241561790.278693968883346X-RAY DIFFRACTION99.9432945846
2.0759-2.10690.3229544561091500.2690966633883333X-RAY DIFFRACTION99.9712973594
2.1069-2.13980.2846457165111720.2431378186483373X-RAY DIFFRACTION99.9717992104
2.1398-2.17490.3010374231241840.2371105064223372X-RAY DIFFRACTION99.8876404494
2.1749-2.21240.261305008761820.2365579975663339X-RAY DIFFRACTION99.9716070415
2.2124-2.25260.288627603392040.2317659138733305X-RAY DIFFRACTION99.9715099715
2.2526-2.2960.2836865998911750.2373433452913342X-RAY DIFFRACTION99.7164729232
2.296-2.34280.282247902121820.2249637515523349X-RAY DIFFRACTION99.8868458274
2.3428-2.39380.3115881381141980.2145025491063334X-RAY DIFFRACTION99.971695443
2.3938-2.44950.2789380618431720.2053909131733367X-RAY DIFFRACTION99.94351878
2.4495-2.51070.2601990519062080.2005907681463339X-RAY DIFFRACTION99.9436460975
2.5107-2.57860.2600733482191710.1958816682593366X-RAY DIFFRACTION99.9434868607
2.5786-2.65450.2827256592761630.1934706406343375X-RAY DIFFRACTION99.9435028249
2.6545-2.74020.2353877210431620.190136071233376X-RAY DIFFRACTION99.9717434303
2.7402-2.83810.2190461784041860.1811253655033396X-RAY DIFFRACTION99.9163179916
2.8381-2.95180.2269305995141910.1816119550763359X-RAY DIFFRACTION99.9155643118
2.9518-3.08610.2371288993681710.1809450167813354X-RAY DIFFRACTION99.9149659864
3.0861-3.24880.2368457917331470.1792962399543429X-RAY DIFFRACTION99.8046329891
3.2488-3.45240.2132053691411790.1669626042863410X-RAY DIFFRACTION99.6667592335
3.4524-3.7190.20264669161690.1555917144413401X-RAY DIFFRACTION100
3.719-4.09320.1529051119411640.1357051906083405X-RAY DIFFRACTION99.8321678322
4.0932-4.68550.1676863716951670.1280908699893447X-RAY DIFFRACTION99.8894416805
4.6855-5.90320.1905844324511970.1573578072663447X-RAY DIFFRACTION99.8629761579
5.9032-95.70360.1926233240872050.1649814500883537X-RAY DIFFRACTION99.2572944297

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