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- PDB-2ohy: X-ray Crystal Structure of Tyrosine Aminomutase from streptomyces... -

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Basic information

Entry
Database: PDB / ID: 2ohy
TitleX-ray Crystal Structure of Tyrosine Aminomutase from streptomyces globisporus
ComponentsTyrosine aminomutase
KeywordsLyase / Transferase / MIO / 4-methylideneimidizole-5-one
Function / homology
Function and homology information


tyrosine 2,3-aminomutase / L-tyrosine 2,3-aminomutase activity / tyrosine ammonia-lyase / tyrosine ammonia-lyase activity / toxin biosynthetic process / antibiotic biosynthetic process
Similarity search - Function
Tyrosine 2,3-aminomutase, putative / 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 ...Tyrosine 2,3-aminomutase, putative / 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
MIO-dependent tyrosine 2,3-aminomutase
Similarity search - Component
Biological speciesStreptomyces globisporus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChristianson, C. / Bruner, S.
CitationJournal: Biochemistry / Year: 2007
Title: The structure of L-tyrosine 2,3-aminomutase from the C-1027 enediyne antitumor antibiotic biosynthetic pathway
Authors: Christianson, C.V. / Montavon, T.J. / Van Lanen, S.G. / Shen, B. / Bruner, S.D.
History
DepositionJan 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 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_ref_seq_dif
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_ref_seq_dif.details
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_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 2.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine aminomutase
B: Tyrosine aminomutase


Theoretical massNumber of molelcules
Total (without water)116,6262
Polymers116,6262
Non-polymers00
Water7,458414
1
A: Tyrosine aminomutase
B: Tyrosine aminomutase

A: Tyrosine aminomutase
B: Tyrosine aminomutase


Theoretical massNumber of molelcules
Total (without water)233,2524
Polymers233,2524
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area33880 Å2
ΔGint-161 kcal/mol
Surface area54960 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)92.597, 146.178, 75.437
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological unit is a tetramer generated from the dimer by the operations: x, y, z and -x, -y, z.

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Components

#1: Protein Tyrosine aminomutase / E.C.5.4.3.6 / ammonia lyase/transferase


Mass: 58312.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces globisporus (bacteria) / Strain: SgcC4 / Plasmid: pET 28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GMG0, tyrosine 2,3-aminomutase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.19 Å3/Da / Density % sol: 43.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 4.4M sodium formate, 0.1M trimethylamine-N-oxide, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 14, 2006
Details: channel-cut Si(111) crystal monochromator followed by a doubly focusing toroidal mirror
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 35786 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0.5 / Redundancy: 6 % / Rmerge(I) obs: 0.132 / Rsym value: 0.132 / Χ2: 1.846 / Net I/σ(I): 8.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.594 / Num. unique all: 3515 / Χ2: 1.693 / % possible all: 99.7

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Phasing

Phasing MRRfactor: 0.598 / Cor.coef. Fo:Fc: 0.171 / Cor.coef. Io to Ic: 0.272
Highest resolutionLowest resolution
Rotation4 Å34.503 Å
Translation4 Å34.503 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT2data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B8F

1b8f


Resolution: 2.5→50 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.263 3435 9.5 %random
Rwork0.192 ---
all0.199 35786 --
obs0.199 34515 95.4 %-
Solvent computationBsol: 37.4 Å2
Displacement parametersBiso mean: 27.652 Å2
Baniso -1Baniso -2Baniso -3
1--4.396 Å20 Å20 Å2
2--8.039 Å20 Å2
3----3.643 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å / Luzzati sigma a obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8021 0 0 414 8435
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_mcbond_it0.941.5
X-RAY DIFFRACTIONc_scbond_it1.4532
X-RAY DIFFRACTIONc_mcangle_it1.5222
X-RAY DIFFRACTIONc_scangle_it2.1112.5
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
2.5-2.590.31792920.2493X-RAY DIFFRACTION351599.7
2.59-2.690.30363090.2384X-RAY DIFFRACTION353799.9
2.69-2.820.31423270.2327X-RAY DIFFRACTION3505100
2.82-2.960.28173050.2028X-RAY DIFFRACTION3539100
2.96-3.150.2893400.2062X-RAY DIFFRACTION3554100
3.15-3.390.28473830.2014X-RAY DIFFRACTION3544100
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep_MDO_7.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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