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- PDB-6h2o: APO structure of Phenylalanine ammonia-lyase from Petroselinum crispum -

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Basic information

Entry
Database: PDB / ID: 6h2o
TitleAPO structure of Phenylalanine ammonia-lyase from Petroselinum crispum
ComponentsPhenylalanine ammonia-lyase 1
KeywordsLYASE / MIO group / Apo structure / plant enzyme
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
Phenylalanine ammonia-lyase 1
Similarity search - Component
Biological speciesPetroselinum crispum (parsley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMolnar, B. / Bata, Z. / Leveles, I. / Poppe, L. / Vertessy, G.B.
Funding support Hungary, Romania, 11items
OrganizationGrant numberCountry
National Research Development and Innovation Office (NKFIH)K119493 Hungary
National Research Development and Innovation Office (NKFIH)NVKP_16-1-2016-0020 Hungary
National Research Development and Innovation Office (NKFIH)2017-1.3.1-VKE-2017-00002 Hungary
National Research Development and Innovation Office (NKFIH)2017-1.3.1-VKE-2017-00013 Hungary
National Research Development and Innovation Office (NKFIH)VEKOP-2.3.2-16-2017-00013 Hungary
National Research Development and Innovation Office (NKFIH)NKP-2018-1.2.1-NKP-2018-00005 Hungary
Ministry of Human CapacitiesBME FIKP-BIO Hungary
Hungarian Academy of SciencesMedinProt grant Hungary
Ministry of Human CapacitiesUNKP-2017-3-III Hungary
National Authority for Scientific Research in Romania (ANCS)ID P_37_273, Cod MySMIS 103413 Romania
National Research Development and Innovation Office (NKFIH)SNN-125637 Hungary
CitationJournal: 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.
History
DepositionJul 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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
Revision 1.2Apr 28, 2021Group: Author supporting evidence / Data collection / Refinement description
Category: pdbx_audit_support / refine ...pdbx_audit_support / refine / refine_ls_shell / reflns
Item: _pdbx_audit_support.funding_organization / _refine.ls_d_res_low ..._pdbx_audit_support.funding_organization / _refine.ls_d_res_low / _refine_ls_shell.d_res_low / _reflns.d_resolution_low
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine_hist / struct_conn
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 / _refine_hist.d_res_low / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)155,6932
Polymers155,6932
Non-polymers00
Water9,890549
1
A: Phenylalanine ammonia-lyase 1
B: Phenylalanine ammonia-lyase 1

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


Theoretical massNumber of molelcules
Total (without water)311,3864
Polymers311,3864
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
Buried area33790 Å2
ΔGint-169 kcal/mol
Surface area78650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.890, 161.120, 141.430
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
11B-1014-

HOH

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Components

#1: Protein Phenylalanine ammonia-lyase 1


Mass: 77846.602 Da / Num. of mol.: 2 / Mutation: C704S, C716S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Petroselinum crispum (parsley) / Gene: PAL1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P24481, phenylalanine ammonia-lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 549 / 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: 2.43 Å3/Da / Density % sol: 49.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 3350 20 m/V%, Potassium formate 0.1 M TRIS 50 mM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→48.1 Å / Num. obs: 104777 / % possible obs: 97.49 % / Redundancy: 4.5 % / Biso Wilson estimate: 28.02 Å2 / Rrim(I) all: 0.144 / Net I/σ(I): 8.78
Reflection shellResolution: 1.9→2 Å

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDS20170720data reduction
XDS20170720data scaling
PHENIX1.13_2998phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F6T

6f6t


Resolution: 1.9→48.1 Å / SU ML: 0.2071 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.8868 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2058 5261 5.02 %
Rwork0.1701 99516 -
obs0.1719 104777 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.59 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9737 0 0 549 10286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00719931
X-RAY DIFFRACTIONf_angle_d0.782113459
X-RAY DIFFRACTIONf_chiral_restr0.04881565
X-RAY DIFFRACTIONf_plane_restr0.00491745
X-RAY DIFFRACTIONf_dihedral_angle_d18.21563640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.30871630.27813061X-RAY DIFFRACTION91.15
1.92-1.940.31181660.26733088X-RAY DIFFRACTION91.79
1.94-1.970.25971720.25613112X-RAY DIFFRACTION91.43
1.97-1.990.30041700.24193045X-RAY DIFFRACTION91.26
1.99-2.020.27211570.23683083X-RAY DIFFRACTION91.45
2.02-2.050.25341620.23453085X-RAY DIFFRACTION91.44
2.05-2.080.25371620.22793076X-RAY DIFFRACTION90.88
2.08-2.110.31111510.20723143X-RAY DIFFRACTION92.95
2.11-2.140.22751690.20163418X-RAY DIFFRACTION99.92
2.14-2.170.21941800.18953351X-RAY DIFFRACTION99.66
2.17-2.210.23711860.18783339X-RAY DIFFRACTION99.6
2.21-2.250.23212000.19183328X-RAY DIFFRACTION99.49
2.25-2.30.20831820.18913382X-RAY DIFFRACTION99.44
2.3-2.340.25271780.18463381X-RAY DIFFRACTION99.55
2.34-2.390.22152040.17573341X-RAY DIFFRACTION99.69
2.39-2.450.22371730.1743391X-RAY DIFFRACTION99.58
2.45-2.510.21582090.17493345X-RAY DIFFRACTION99.64
2.51-2.580.22031720.16963378X-RAY DIFFRACTION99.61
2.58-2.650.21651640.1753385X-RAY DIFFRACTION99.66
2.65-2.740.22751540.17833378X-RAY DIFFRACTION99.38
2.74-2.840.19251870.16943384X-RAY DIFFRACTION99.58
2.84-2.950.19341900.1693403X-RAY DIFFRACTION99.25
2.95-3.090.21741790.17443373X-RAY DIFFRACTION99.52
3.09-3.250.20451500.16593437X-RAY DIFFRACTION99.39
3.25-3.450.18371760.15883411X-RAY DIFFRACTION99.83
3.45-3.720.18571640.15023455X-RAY DIFFRACTION99.97
3.72-4.090.15811700.13513426X-RAY DIFFRACTION99.89
4.09-4.680.15771670.12723475X-RAY DIFFRACTION99.92
4.68-5.90.19932000.15753473X-RAY DIFFRACTION99.84
5.9-48.10.19182040.17073569X-RAY DIFFRACTION99.32

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