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- PDB-3vbi: Crystal Structure of AntD, an N-acyltransferase from Bacillus cer... -

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Basic information

Entry
Database: PDB / ID: 3vbi
TitleCrystal Structure of AntD, an N-acyltransferase from Bacillus cereus in complex with dTDP-4-amino-4,6-dideoxyglucose and Coenzyme A
ComponentsGalactoside O-acetyltransferase
KeywordsTRANSFERASE / anthrose / acylated sugar / left-handed beta helix / sugar N-acylation
Function / homologyHexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / 3 Solenoid / Mainly Beta / dTDP-4-amino-4,6-dideoxyglucose / BICARBONATE ION / COENZYME A / :
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKubiak, R.L. / Holden, H.M.
CitationJournal: Biochemistry / Year: 2012
Title: Structural Studies of AntD: An N-Acyltransferase Involved in the Biosynthesis of d-Anthrose.
Authors: Kubiak, R.L. / Holden, H.M.
History
DepositionJan 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Galactoside O-acetyltransferase
C: Galactoside O-acetyltransferase
E: Galactoside O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,42013
Polymers68,2573
Non-polymers4,16310
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14140 Å2
ΔGint-66 kcal/mol
Surface area20180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.115, 71.115, 138.179
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Protein , 1 types, 3 molecules ACE

#1: Protein Galactoside O-acetyltransferase / AntD


Mass: 22752.293 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: SJ1 / Gene: antd, BCSJ1_02085 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 DE3
References: UniProt: D7WGJ0, galactoside O-acetyltransferase

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Non-polymers , 5 types, 308 molecules

#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-0FX / dTDP-4-amino-4,6-dideoxyglucose


Mass: 547.345 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H27N3O14P2
#4: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CHO3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.56 Å3/Da / Density % sol: 51.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 25% pentaerythritol ethoxylate (3/4 EO/OH), 2% isopropanol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: May 9, 2011 / Details: Montel
RadiationMonochromator: Nickel filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→38.659 Å / Num. all: 63508 / Num. obs: 57751 / % possible obs: 90.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 11.8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 1.6 / Num. unique all: 7460 / Rsym value: 0.249 / % possible all: 78

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
REFMAC5.5.0109refinement
SAINTdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN-HOUSE MIR MODEL

Resolution: 1.8→38.659 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.476 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24498 2893 5 %RANDOM
Rwork0.19821 ---
obs0.20049 54826 90.97 %-
all-57719 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.478 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--0.2 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.8→38.659 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4311 0 262 298 4871
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224696
X-RAY DIFFRACTIONr_angle_refined_deg2.2772.0286381
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6385567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.71424.311167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.23915813
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5971515
X-RAY DIFFRACTIONr_chiral_restr0.1850.2727
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213317
X-RAY DIFFRACTIONr_mcbond_it1.4061.52778
X-RAY DIFFRACTIONr_mcangle_it2.28124489
X-RAY DIFFRACTIONr_scbond_it3.74631918
X-RAY DIFFRACTIONr_scangle_it5.2394.51886
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 185 -
Rwork0.355 3355 -
obs--75.82 %

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