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- PDB-2o7e: Tyrosine ammonia-lyase from Rhodobacter sphaeroides (His89Phe var... -

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Basic information

Entry
Database: PDB / ID: 2o7e
TitleTyrosine ammonia-lyase from Rhodobacter sphaeroides (His89Phe variant), bound to 2-aminoindan-2-phosphonic acid
ComponentsPutative histidine ammonia-lyase
KeywordsLYASE / Methylidene imidazolone prosthetic group
Function / homology
Function and homology information


tyrosine ammonia-lyase / tyrosine ammonia-lyase activity / phenylpropanoid biosynthetic process / tyrosine catabolic process / protein homotetramerization / identical protein binding
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
Chem-PMI / Tyrosine ammonia-lyase
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLouie, G.V. / Bowman, M.E. / Moffitt, M.C. / Baiga, T.J. / Moore, B.S. / Noel, J.P.
CitationJournal: Chem.Biol. / Year: 2006
Title: Structural determinants and modulation of substrate specificity in phenylalanine-tyrosine ammonia-lyases.
Authors: Louie, G.V. / Bowman, M.E. / Moffitt, M.C. / Baiga, T.J. / Moore, B.S. / Noel, J.P.
History
DepositionDec 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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_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 / _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 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999Sequence Residue MDO is autocatalytically formed by internal tripeptide segment Ala149-Ser150-Gly151

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative histidine ammonia-lyase
B: Putative histidine ammonia-lyase
C: Putative histidine ammonia-lyase
D: Putative histidine ammonia-lyase
E: Putative histidine ammonia-lyase
F: Putative histidine ammonia-lyase
G: Putative histidine ammonia-lyase
H: Putative histidine ammonia-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)441,34316
Polymers439,6388
Non-polymers1,7058
Water55,6483089
1
A: Putative histidine ammonia-lyase
B: Putative histidine ammonia-lyase
C: Putative histidine ammonia-lyase
D: Putative histidine ammonia-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,6728
Polymers219,8194
Non-polymers8534
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33360 Å2
ΔGint-153 kcal/mol
Surface area56760 Å2
MethodPISA
2
E: Putative histidine ammonia-lyase
F: Putative histidine ammonia-lyase
G: Putative histidine ammonia-lyase
H: Putative histidine ammonia-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,6728
Polymers219,8194
Non-polymers8534
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33330 Å2
ΔGint-154 kcal/mol
Surface area56410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.571, 154.838, 164.526
Angle α, β, γ (deg.)90.00, 94.16, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe 222-symmetric homotetramer includes chains A, B, C, and D. / The 222-symmetric homotetramer includes chains E, F, G, and H.

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Components

#1: Protein
Putative histidine ammonia-lyase


Mass: 54954.715 Da / Num. of mol.: 8 / Mutation: H89F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: hutH / Plasmid: pHis8 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q3IWB0, EC: 4.3.1.-
#2: Chemical
ChemComp-PMI / (2-AMINO-2,3-DIHYDRO-1H-INDEN-2-YL)PHOSPHONIC ACID / 2-AMINOINDAN-2-PHOSPHONIC ACID


Mass: 213.170 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C9H12NO3P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3089 / 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: 2.53 Å3/Da / Density % sol: 51.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M MOPSO (pH 7.0), 7% (w/v) polyethylene glycol 8000, 0.3 M ammonium acetate, 2 mM dithiothreitol, 35 mM cyclohexylbutanoyl-N-hydroxyethylglucamide , VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 1, 2006
RadiationMonochromator: Single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.75→500 Å / Num. obs: 422417 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 9.3
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 1.9 / Num. unique all: 52267 / % possible all: 82.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2o6y (tyrosine ammonia-lyase from Rhodobacter sphaeroides)

2o6y


Resolution: 1.75→500 Å / Isotropic thermal model: Isotropic / Cross valid method: Random / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2098 21241 -Random
Rwork0.1894 ---
all-438411 --
obs-420387 96.4 %-
Displacement parametersBiso mean: 21.3 Å2
Refinement stepCycle: LAST / Resolution: 1.75→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30470 0 112 3089 33671
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.234
X-RAY DIFFRACTIONc_mcbond_it1.43
X-RAY DIFFRACTIONc_mcangle_it2.006
X-RAY DIFFRACTIONc_scbond_it2.539
X-RAY DIFFRACTIONc_scangle_it3.828
LS refinement shellResolution: 1.75→1.83 Å
RfactorNum. reflection% reflection
Rfree0.3123 2141 -
Rwork0.2928 --
obs-39957 82.2 %

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