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- PDB-2o7d: Tyrosine ammonia-lyase from Rhodobacter sphaeroides, complexed wi... -

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Basic information

Entry
Database: PDB / ID: 2o7d
TitleTyrosine ammonia-lyase from Rhodobacter sphaeroides, complexed with caffeate
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
CAFFEIC ACID / Tyrosine ammonia-lyase
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 10, 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 1.3Aug 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
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)441,00716
Polymers439,5668
Non-polymers1,4418
Water58,0623223
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)220,5038
Polymers219,7834
Non-polymers7214
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33420 Å2
ΔGint-140 kcal/mol
Surface area56720 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)220,5038
Polymers219,7834
Non-polymers7214
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33350 Å2
ΔGint-141 kcal/mol
Surface area56430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.614, 154.895, 164.162
Angle α, β, γ (deg.)90.00, 94.06, 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: 54945.688 Da / Num. of mol.: 8 / Fragment: Tyrosine ammonia-lyase
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-DHC / CAFFEIC ACID / 3,4-DIHYDROXYCINNAMIC ACID / Caffeic acid


Mass: 180.157 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C9H8O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3223 / 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: 2.53 Å3/Da / Density % sol: 51.31 %
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: 1.9→500 Å / Num. obs: 338640 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 8.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 2.4 / % possible all: 97.5

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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: 1.9→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
Rfree0.1978 17123 -Random
Rwork0.1752 ---
all-367641 --
obs-338602 98.9 %-
Displacement parametersBiso mean: 21.9 Å2
Refinement stepCycle: LAST / Resolution: 1.9→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30462 0 104 3223 33789
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.178
X-RAY DIFFRACTIONc_mcbond_it1.453
X-RAY DIFFRACTIONc_mcangle_it1.987
X-RAY DIFFRACTIONc_scbond_it2.518
X-RAY DIFFRACTIONc_scangle_it3.722
LS refinement shellResolution: 1.9→1.99 Å
RfactorNum. reflection% reflection
Rfree0.2831 2148 -
Rwork0.2534 --
obs-39427 97.5 %

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