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- PDB-9bgr: X-ray structure of the aminotransferase from Vibrio vulnificus re... -

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Basic information

Entry
Database: PDB / ID: 9bgr
TitleX-ray structure of the aminotransferase from Vibrio vulnificus responsible for the biosynthesis of 2,3-diacetamido-4-amino-2,3,4-trideoxy-arabinose in the presence of its external aldimine with 2,3-diacetamido-4-amino-2,3,4-trideoxy-l-arabinose
Componentsaminotransferase
KeywordsTRANSFERASE / aminotransferase / lipopolysaccharide / pyridoxal 5'-phosphate / 2 / 3 / 4-triacetamido-2 / 4-trideoxy-L-arabinose / Vibrio vulnificus
Function / homology: / TRIETHYLENE GLYCOL
Function and homology information
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.05 Å
AuthorsFait, D.J. / Thoden, J.B. / Holden, H.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM134643 United States
CitationJournal: To Be Published
Title: Biochemical Investigation of an Aminotransferase Required for the Production of 2,3,4-triacetamido-2,3,4-trideoxy-L-arabinose
Authors: Fait, D.J. / Bockhaus, N.J. / Dunsirn, M.M. / Thoden, J.B. / Holden, H.M.
History
DepositionApr 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: aminotransferase
B: aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,93222
Polymers83,7612
Non-polymers3,17120
Water17,222956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7930 Å2
ΔGint22 kcal/mol
Surface area26390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.958, 53.048, 70.267
Angle α, β, γ (deg.)83.00, 82.17, 74.36
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein aminotransferase


Mass: 41880.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2

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Non-polymers , 5 types, 976 molecules

#2: Chemical ChemComp-A1APE / (2R,3R,4R,5R)-3,4-diacetamido-5-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methoxy)oxan-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxyoxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name)


Mass: 849.522 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H38N5O21P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 956 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: protein incubated with 5.0 mM UDP-4-amino-2,3-diacetoamido-2,3,4-trideoxy-L-arabinose and 1.0 mM PLP. Precipitant: 15-20% (w/v) poly(ethylene glycol) 5000, 200 mM NaCl, and 100 mM MES (pH 6.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Feb 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.05→50 Å / Num. obs: 330200 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Redundancy: 4.6 % / Rsym value: 0.087 / Net I/σ(I): 7.7
Reflection shellResolution: 1.05→1.15 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 73676 / Rsym value: 0.481 / % possible all: 87.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
SAINTdata reduction
SADABSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.05→38.96 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.26 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17728 16781 5.1 %RANDOM
Rwork0.15937 ---
obs0.16028 313419 97.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.476 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0.02 Å2-0.06 Å2
2---0.03 Å20.07 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.05→38.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5671 0 204 956 6831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0126232
X-RAY DIFFRACTIONr_bond_other_d00.0166006
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.6778490
X-RAY DIFFRACTIONr_angle_other_deg0.5281.5813866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4565813
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.702532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.976101052
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0820.2976
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027263
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021359
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6650.6943046
X-RAY DIFFRACTIONr_mcbond_other0.6650.6943046
X-RAY DIFFRACTIONr_mcangle_it0.9651.2473823
X-RAY DIFFRACTIONr_mcangle_other0.9651.2473824
X-RAY DIFFRACTIONr_scbond_it0.990.9423186
X-RAY DIFFRACTIONr_scbond_other0.990.9423187
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3041.6214630
X-RAY DIFFRACTIONr_long_range_B_refined2.78913.067475
X-RAY DIFFRACTIONr_long_range_B_other2.0879.877144
X-RAY DIFFRACTIONr_rigid_bond_restr4.787312238
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.05→1.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 1105 -
Rwork0.36 20056 -
obs--84.52 %

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