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- PDB-2rjs: SgTAM bound to substrate mimic -

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Basic information

Entry
Database: PDB / ID: 2rjs
TitleSgTAM bound to substrate mimic
ComponentsTyrosine aminomutase
KeywordsISOMERASE / 4-methylidene imidazole / MIO / aminomutase / C-1027
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
Chem-296 / MIO-dependent tyrosine 2,3-aminomutase
Similarity search - Component
Biological speciesStreptomyces globisporus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsMontavon, T.J. / Christianson, C.V. / Bruner, S.D.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2008
Title: Design and characterization of mechanism-based inhibitors for the tyrosine aminomutase SgTAM.
Authors: Montavon, T.J. / Christianson, C.V. / Festin, G.M. / Shen, B. / Bruner, S.D.
History
DepositionOct 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
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_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_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine aminomutase
B: Tyrosine aminomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,8004
Polymers116,3382
Non-polymers4622
Water7,170398
1
A: Tyrosine aminomutase
B: Tyrosine aminomutase
hetero molecules

A: Tyrosine aminomutase
B: Tyrosine aminomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,6008
Polymers232,6754
Non-polymers9254
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area33690 Å2
ΔGint-165 kcal/mol
Surface area54540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.494, 146.286, 75.009
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 58168.766 Da / Num. of mol.: 2 / Fragment: tyrosine aminomutase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces globisporus (bacteria) / Gene: SgcC4 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GMG0, tyrosine 2,3-aminomutase
#2: Chemical ChemComp-296 / (3R)-3-amino-2,2-difluoro-3-(4-methoxyphenyl)propanoic acid


Mass: 231.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H11F2NO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 4.4 M sodium formate, 100 mM TMAO, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 3, 2007
Details: channel-cut Si(111) crystal monochromator followed by a doubly focusing toroidal mirror
RadiationMonochromator: Si(iii)crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. obs: 40450 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0.5 / Redundancy: 5.5 % / Rmerge(I) obs: 0.116 / Χ2: 3.764 / Net I/σ(I): 12.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 4.1 / Num. unique all: 3992 / Χ2: 2.451 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
CNSphasing
RefinementStarting model: pdb entry 2OHY

2ohy


Resolution: 2.4→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 3812 9.4 %random
Rwork0.182 ---
all0.188 40450 --
obs0.188 37827 93.3 %-
Solvent computationBsol: 46.565 Å2
Displacement parametersBiso mean: 37.352 Å2
Baniso -1Baniso -2Baniso -3
1--6.845 Å20 Å20 Å2
2--6.695 Å20 Å2
3---0.151 Å2
Refinement stepCycle: LAST / Resolution: 2.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8021 0 32 398 8451
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_mcbond_it1.1751.5
X-RAY DIFFRACTIONc_scbond_it1.8932
X-RAY DIFFRACTIONc_mcangle_it1.8022
X-RAY DIFFRACTIONc_scangle_it2.7672.5
LS refinement shell
Resolution (Å)Rfactor RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
2.4-2.490.4790.6X-RAY DIFFRACTION3992100
2.49-2.590.5110.405X-RAY DIFFRACTION4007100
2.6-2.840.3020.26X-RAY DIFFRACTION3983100
3.26-3.580.1320.129X-RAY DIFFRACTION4046100
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep_MDO_7.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3newmetyr.param

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