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

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Basic information

Entry
Database: PDB / ID: 9bgp
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 internal aldimine
Componentsaminotransferase
KeywordsTRANSFERASE / aminotransferase / lipopolysaccharide / pyridoxal 5'-phosphate / 2 / 3 / 4-triacetamido-2 / 4-trideoxy-L-arabinose / Vibrio vulnificus
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.25 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.B. / 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

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Assembly

Deposited unit
A: aminotransferase
B: aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,27318
Polymers84,3332
Non-polymers94016
Water15,871881
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-20 kcal/mol
Surface area26300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.110, 53.116, 70.322
Angle α, β, γ (deg.)82.59, 82.56, 74.40
Int Tables number1
Space group name H-MP1

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Components

#1: Protein aminotransferase


Mass: 42166.719 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
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 881 / Source method: isolated from a natural source / Formula: H2O
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: 44.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 8-12% (w/v) poly(ethylene glycol) 8000, 200 mM LiCl, and 100 mM Homo-PIPES (pH 5.0)

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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: Jul 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 199391 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Redundancy: 4.9 % / Rsym value: 0.073 / Net I/σ(I): 10.7
Reflection shellResolution: 1.25→1.35 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 39859 / Rsym value: 0.377 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.25→33.45 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 0.776 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18813 10023 5 %RANDOM
Rwork0.16746 ---
obs0.16848 189368 98.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.376 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.25→33.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5673 0 58 881 6612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125901
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165678
X-RAY DIFFRACTIONr_angle_refined_deg1.521.6497989
X-RAY DIFFRACTIONr_angle_other_deg0.5111.56613056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4755751
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.688529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09310976
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0790.2920
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026874
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021284
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_it1.0030.6972977
X-RAY DIFFRACTIONr_mcbond_other0.990.6962977
X-RAY DIFFRACTIONr_mcangle_it1.5691.2463719
X-RAY DIFFRACTIONr_mcangle_other1.5711.2473720
X-RAY DIFFRACTIONr_scbond_it2.3960.9652924
X-RAY DIFFRACTIONr_scbond_other2.3970.9662925
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6791.6344265
X-RAY DIFFRACTIONr_long_range_B_refined4.98811.237040
X-RAY DIFFRACTIONr_long_range_B_other4.6268.656754
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 680 -
Rwork0.316 13308 -
obs--93.58 %

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