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- PDB-2zq5: Crystal structure of sulfotransferase STF1 from Mycobacterium tub... -

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Basic information

Entry
Database: PDB / ID: 2zq5
TitleCrystal structure of sulfotransferase STF1 from Mycobacterium tuberculosis H37Rv (type1 form)
ComponentsPutative uncharacterized protein
KeywordsTRANSFERASE / sulfotransferase fold
Function / homology: / Sulfotransferase family / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta / Sulfotransferase
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsTanaka, S. / Kimura, M. / Kakuta, Y.
CitationJournal: To be Published
Title: Crystal structure of sulfotransferase STF1 from Mycobacterium tuberculosis H37Rv
Authors: Tanaka, S. / Kimura, M. / Kakuta, Y.
History
DepositionAug 6, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 13, 2019Group: Data collection / Database references / Category: reflns / struct_ref_seq_dif
Item: _reflns.pdbx_Rmerge_I_obs / _struct_ref_seq_dif.details
Revision 1.3Dec 11, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rsym_value / _reflns_shell.pdbx_Rsym_value
Revision 1.4Mar 13, 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 uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)43,3891
Polymers43,3891
Non-polymers00
Water12,683704
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.864, 95.761, 48.038
Angle α, β, γ (deg.)90.00, 106.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative uncharacterized protein / sulfotransferase / stf1


Mass: 43388.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT3632, Rv3529c / Plasmid: pGEX4T3 / Production host: Escherichia coli (E. coli) / References: UniProt: P71872
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 704 / 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: 2.08 Å3/Da / Density % sol: 40.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 20% PEG 3350, 0.1M bis-tris pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 56164 / Num. obs: 56164 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 5.8 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 26.1
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.125 / Mean I/σ(I) obs: 10 / Num. unique all: 5474 / % possible all: 98.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 2→46.08 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 481773.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.198 1196 5 %RANDOM
Rwork0.176 ---
obs0.176 23701 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.1825 Å2 / ksol: 0.365925 e/Å3
Displacement parametersBiso mean: 17 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å20 Å2-0.69 Å2
2---0.1 Å20 Å2
3----1.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å0.04 Å
Refinement stepCycle: LAST / Resolution: 2→46.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2913 0 0 704 3617
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.192 225 5.7 %
Rwork0.17 3741 -
obs--99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param

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