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- PDB-5xxr: Crystal structure of selenomethionine labelled RIBT from Bacillus... -

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Basic information

Entry
Database: PDB / ID: 5xxr
TitleCrystal structure of selenomethionine labelled RIBT from Bacillus subtilis
ComponentsProtein RibT
KeywordsTRANSFERASE / Riboflavin / CoA / GNAT / acetylation
Function / homologyriboflavin biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / COENZYME A / Protein RibT
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.647 Å
AuthorsSrivastava, R. / Karthikeyan, S.
Funding support India, 1items
OrganizationGrant numberCountry
CSIRBSC-0104 India
CitationJournal: J. Struct. Biol. / Year: 2018
Title: Structural characterization of ribT from Bacillus subtilis reveals it as a GCN5-related N-acetyltransferase.
Authors: Srivastava, R. / Kaur, A. / Sharma, C. / Karthikeyan, S.
History
DepositionJul 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 13, 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
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: Protein RibT
B: Protein RibT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3364
Polymers31,8002
Non-polymers1,5352
Water41423
1
A: Protein RibT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6682
Polymers15,9001
Non-polymers7681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint0 kcal/mol
Surface area7550 Å2
MethodPISA
2
B: Protein RibT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6682
Polymers15,9001
Non-polymers7681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-2 kcal/mol
Surface area6260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.572, 57.550, 73.088
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein RibT


Mass: 15900.222 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: ribT, BSU23240 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P17622, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.46 % / Description: Two dimensional plate like
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% 2.7M sodium malonate, 80% 2.1M Malic acid / PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97883 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 23, 2015 / Details: Mirror
RadiationMonochromator: SI III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97883 Å / Relative weight: 1
ReflectionResolution: 2.63→50 Å / Num. obs: 6986 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 25.4 % / Biso Wilson estimate: 53 Å2 / CC1/2: 0.93 / Rmerge(I) obs: 0.191 / Net I/σ(I): 23.1
Reflection shellResolution: 2.63→2.68 Å / Redundancy: 16.1 % / Rmerge(I) obs: 0.906 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 315 / CC1/2: 0.68 / % possible all: 92.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.647→36.544 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2763 348 4.99 %Random
Rwork0.2238 ---
obs0.2264 6970 98.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.647→36.544 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1842 0 96 23 1961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021974
X-RAY DIFFRACTIONf_angle_d0.412681
X-RAY DIFFRACTIONf_dihedral_angle_d16.871187
X-RAY DIFFRACTIONf_chiral_restr0.04295
X-RAY DIFFRACTIONf_plane_restr0.004338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6467-3.33420.32321740.24563176X-RAY DIFFRACTION96
3.3342-36.54750.25811740.21663446X-RAY DIFFRACTION100

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