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- PDB-3itw: Crystal structure of TioX from Micromonospora sp. ML1 -

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Basic information

Entry
Database: PDB / ID: 3itw
TitleCrystal structure of TioX from Micromonospora sp. ML1
ComponentsProtein tioX
KeywordsPEPTIDE BINDING PROTEIN / bleomycin resistance fold / bisintercalator / solvent-exposed Trp residue / thiocoraline / PROTEIN BINDING
Function / homology
Function and homology information


Signal recognition particle alu RNA binding heterodimer, srp9/1 - #120 / Signal recognition particle alu RNA binding heterodimer, srp9/1 - #110 / Signal recognition particle alu RNA binding heterodimer, srp9/1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
VOC domain-containing protein
Similarity search - Component
Biological speciesMicromonospora sp. ML1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Se MAD/MIR / Resolution: 2.15 Å
AuthorsBiswas, T. / Garneau-Tsodikova, S. / Tsodikov, O.V.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: A New Scaffold of an Old Protein Fold Ensures Binding to the Bisintercalator Thiocoraline.
Authors: Biswas, T. / Zolova, O.E. / Lombo, F. / de la Calle, F. / Salas, J.A. / Tsodikov, O.V. / Garneau-Tsodikova, S.
History
DepositionAug 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein tioX
B: Protein tioX


Theoretical massNumber of molelcules
Total (without water)30,9412
Polymers30,9412
Non-polymers00
Water1,820101
1
A: Protein tioX
B: Protein tioX

A: Protein tioX
B: Protein tioX


Theoretical massNumber of molelcules
Total (without water)61,8834
Polymers61,8834
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+1/2,y,-z+3/41
Buried area8080 Å2
ΔGint-64 kcal/mol
Surface area22210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.321, 109.321, 143.333
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Protein tioX


Mass: 15470.679 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora sp. ML1 (bacteria) / Gene: tioX / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q333U2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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

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Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Reservoir solution: 400 mM sodium potassium tartrate, 25 mM ammonium sulfate, 2% glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONAPS 21-ID-D1
SYNCHROTRONAPS 23-ID-B2
DetectorDate: Aug 16, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.15→40 Å / Num. obs: 47329

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: Se MAD/MIR / Resolution: 2.15→40 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.922 / SU B: 11.843 / SU ML: 0.153 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26786 1205 5.1 %RANDOM
Rwork0.2323 ---
obs0.23403 22426 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.024 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.15→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1957 0 0 101 2058
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212004
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.171.9322723
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2355246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.86421.91594
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.96415314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9311522
X-RAY DIFFRACTIONr_chiral_restr0.080.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021534
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.180.2801
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21316
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2109
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.280
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5971.51259
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.94221974
X-RAY DIFFRACTIONr_scbond_it1.4063852
X-RAY DIFFRACTIONr_scangle_it2.2434.5749
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 86 -
Rwork0.287 1541 -
obs--95.04 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.03310.96190.01692.2253-0.01784.17180.09390.45140.46590.01350.1734-0.0151-0.03740.3116-0.2673-0.4302-0.0612-0.0787-0.1947-0.0689-0.230838.10960.20853.138
24.5328-0.71381.48224.8645-1.96925.160.0336-0.8681-0.5932-0.00950.25950.28010.4367-0.5357-0.2932-0.4598-0.0777-0.1923-0.02280.3184-0.411420.00441.59371.197
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 120
2X-RAY DIFFRACTION2B1 - 134

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