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- PDB-1xdz: Crystal Structure of Gram_Positive Bacillus subtilis Glucose inhi... -

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Basic information

Entry
Database: PDB / ID: 1xdz
TitleCrystal Structure of Gram_Positive Bacillus subtilis Glucose inhibited Division protein B (gidB), Structural genomics, MCSG
ComponentsMethyltransferase gidB
KeywordsTRANSFERASE / MCSG / Protein Structure Initiative / Structural Genomics / methyltransferase fold / GidB / PSI / Midwest Center for Structural Genomics
Function / homology
Function and homology information


rRNA (guanine-N7-)-methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / cytosol
Similarity search - Function
rRNA small subunit methyltransferase G / rRNA small subunit methyltransferase G / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribosomal RNA small subunit methyltransferase G
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsZhang, R. / Wu, R. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The 1.6A crystal ctructure of Gram-positive Bacillus subtilis glucose inhibited division protein B (gidB)
Authors: Zhang, R. / Wu, R. / Collart, F. / Joachimiak, A.
History
DepositionSep 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Methyltransferase gidB


Theoretical massNumber of molelcules
Total (without water)27,1041
Polymers27,1041
Non-polymers00
Water3,801211
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.496, 58.164, 51.207
Angle α, β, γ (deg.)90.00, 123.40, 90.00
Int Tables number5
Space group name H-MC121
Detailsthe biological assembly is monomer

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Components

#1: Protein Methyltransferase gidB / Glucose inhibited division protein B


Mass: 27104.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: gidB / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P25813, Transferases; Transferring one-carbon groups
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.037 Å3/Da / Density % sol: 37.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Mg chloride, 0.1M tris hydrochloride, 25% PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97835 Å
DetectorType: SBC-2 / Detector: CCD / Date: Dec 16, 2003 / Details: mirrors
RadiationMonochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97835 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 28822 / Num. obs: 27352 / % possible obs: 94.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.1 % / Rmerge(I) obs: 0.076 / Rsym value: 0.19 / Net I/σ(I): 28.6
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 1.52 / Num. unique all: 1760 / % possible all: 61.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→45.69 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.03 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.116 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22052 1377 5 %RANDOM
Rwork0.20207 ---
all0.20306 28822 --
obs0.20306 27352 94.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.441 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2---0.8 Å20 Å2
3---0.56 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.6→45.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1895 0 0 211 2106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221931
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.9782608
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0825236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.6824.76786
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48215360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0371510
X-RAY DIFFRACTIONr_chiral_restr0.0850.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021426
X-RAY DIFFRACTIONr_nbd_refined0.2090.21142
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21359
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.279
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.26
X-RAY DIFFRACTIONr_mcbond_it0.861.51220
X-RAY DIFFRACTIONr_mcangle_it1.37821931
X-RAY DIFFRACTIONr_scbond_it2.0663783
X-RAY DIFFRACTIONr_scangle_it3.3014.5677
LS refinement shellResolution: 1.598→1.639 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 63 -
Rwork0.298 1156 -
obs--58.24 %

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