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- PDB-1jsx: Crystal Structure of the Escherichia coli Glucose-Inhibited Divis... -

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Basic information

Entry
Database: PDB / ID: 1jsx
TitleCrystal Structure of the Escherichia coli Glucose-Inhibited Division Protein B (GidB)
ComponentsGlucose-inhibited division protein B
KeywordsUNKNOWN FUNCTION / methyltransferase fold / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


16S rRNA (guanine527-N7)-methyltransferase / rRNA (guanine-N7-)-methyltransferase activity / rRNA base methylation / 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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsRomanowski, M.J. / Bonanno, J.B. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Proteins / Year: 2002
Title: Crystal structure of the Escherichia coli glucose-inhibited division protein B (GidB) reveals a methyltransferase fold.
Authors: Romanowski, M.J. / Bonanno, J.B. / Burley, S.K.
History
DepositionAug 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.4Feb 7, 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: Glucose-inhibited division protein B


Theoretical massNumber of molelcules
Total (without water)23,4611
Polymers23,4611
Non-polymers00
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.914, 53.914, 150.592
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Glucose-inhibited division protein B


Mass: 23461.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: gidB / Plasmid: pGEX6P1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0A6U5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 15% PEG4000, 10% isopropanol, 0.1M sodium citrate pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMHEPES1droppH7.0
2100 mM1dropKCl
33 mMdithiothreitol1drop
424 mg/mlprotein1drop
50.1 Msodium citrate1reservoirpH6.5
615 %PEG40001reservoir
710 %isopropanol1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11501
21501
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X9A10.97903, 0.97927
SYNCHROTRONNSLS X9A20.98399
Detector
TypeIDDetectorDateDetails
MARRESEARCH1CCDOct 20, 2000Primary Aperture - 7.4 m from source. Be Windows front end - 0.020" thick, 7.1 m from source exit window - 0.010" thick. White X-Ray Beam.
MARRESEARCH2CCDMar 28, 2001Primary Aperture - 7.4 m from source. Be Windows front end - 0.020" thick, 7.1 m from source exit window: 0.010" thick. White X-Ray Beam.
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111MADMx-ray1
2Si 111SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979031
20.979271
30.983991
ReflectionResolution: 2.4→30 Å / Num. all: 9170 / Num. obs: 9170 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 27.6 Å2 / Rsym value: 0.078
Reflection shellResolution: 2.4→2.55 Å / % possible all: 98.1
Reflection
*PLUS
Lowest resolution: 30 Å

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.4→17.97 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 663404.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 936 10.2 %RANDOM
Rwork0.24 ---
all0.2345 9170 --
obs0.24 9170 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.6735 Å2 / ksol: 0.375812 e/Å3
Displacement parametersBiso mean: 36.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å20 Å20 Å2
2--1.38 Å20 Å2
3----2.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.4→17.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1542 0 0 127 1669
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.441.5
X-RAY DIFFRACTIONc_mcangle_it2.382
X-RAY DIFFRACTIONc_scbond_it2.712
X-RAY DIFFRACTIONc_scangle_it3.492.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.329 144 9.7 %
Rwork0.231 1338 -
obs--98.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 18 Å / Rfactor obs: 0.24 / Rfactor Rfree: 0.275 / Rfactor Rwork: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81
LS refinement shell
*PLUS
Rfactor Rfree: 0.329 / Rfactor Rwork: 0.231 / Rfactor obs: 0.231

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