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- PDB-3ry0: Crystal structure of TomN, a 4-Oxalocrotonate Tautomerase homolog... -

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Basic information

Entry
Database: PDB / ID: 3ry0
TitleCrystal structure of TomN, a 4-Oxalocrotonate Tautomerase homologue in Tomaymycin biosynthetic pathway
ComponentsPutative tautomerase
KeywordsISOMERASE / 4 oxalocrotonate tautomerase family / tautomerase
Function / homology4-oxalocrotonate tautomerase / Tautomerase enzyme / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / isomerase activity / 2-Layer Sandwich / Alpha Beta / Putative tautomerase
Function and homology information
Biological speciesStreptomyces achromogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsZhang, Y. / Yan, W.P. / Li, W.Z. / Whitman, C.P.
CitationJournal: Biochemistry / Year: 2011
Title: Kinetic, Crystallographic, and Mechanistic Characterization of TomN: Elucidation of a Function for a 4-Oxalocrotonate Tautomerase Homologue in the Tomaymycin Biosynthetic Pathway.
Authors: Burks, E.A. / Yan, W. / Johnson, W.H. / Li, W. / Schroeder, G.K. / Min, C. / Gerratana, B. / Zhang, Y. / Whitman, C.P.
History
DepositionMay 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2011Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative tautomerase
B: Putative tautomerase


Theoretical massNumber of molelcules
Total (without water)13,8802
Polymers13,8802
Non-polymers00
Water3,099172
1
A: Putative tautomerase
B: Putative tautomerase

A: Putative tautomerase
B: Putative tautomerase

A: Putative tautomerase
B: Putative tautomerase


Theoretical massNumber of molelcules
Total (without water)41,6396
Polymers41,6396
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area11760 Å2
ΔGint-62 kcal/mol
Surface area16660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.637, 117.637, 117.637
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11B-134-

HOH

21B-162-

HOH

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Components

#1: Protein Putative tautomerase


Mass: 6939.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces achromogenes (bacteria) / Gene: tomN / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (Gold) / References: UniProt: C0LTT5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.4449.66
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2981vapor diffusion, sitting drop4.5100mM magnesium acetate, 100mM sodium acetate, 5%-21% PEG8000, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
2982vapor diffusion, sitting drop4.5100mM calcium acetate, 100mM sodium acetate, 1%-13% PEG4000, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2009 / Details: mirror
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→83.18 Å / Num. all: 27574 / Num. obs: 27574 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 35.7 % / Rsym value: 0.068 / Net I/σ(I): 1.8
Reflection shellResolution: 1.4→1.42 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.163 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25116 1379 5 %RANDOM
Rwork0.2207 ---
obs0.22222 26052 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.15 Å2
Refinement stepCycle: LAST / Resolution: 1.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms964 0 0 172 1136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.022981
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3551.9791338
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6675126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.81221.540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.19915153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.031514
X-RAY DIFFRACTIONr_chiral_restr0.1680.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021740
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5921.5640
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.5921033
X-RAY DIFFRACTIONr_scbond_it4.0923341
X-RAY DIFFRACTIONr_scangle_it6.2834.5305
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.472 96 -
Rwork0.371 1921 -
obs--100 %

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