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- PDB-8vr6: crystal structure of the Pcryo_0619 N-acetryltransferase from Psy... -

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Basic information

Entry
Database: PDB / ID: 8vr6
Titlecrystal structure of the Pcryo_0619 N-acetryltransferase from Psychrobacter cryohalolentis K5 in the presence of CoA-disulfide
ComponentsAcetyltransferase, putative
KeywordsTRANSFERASE / psychrobacter / n-acetyltransferase / 2 / 3 / 4-triacetoamido-2 / 4-trideoxy-l-arabinose
Function / homology
Function and homology information


acyltransferase activity
Similarity search - Function
: / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily
Similarity search - Domain/homology
Chem-5NG / Acetyltransferase, putative
Similarity search - Component
Biological speciesPsychrobacter cryohalolentis K5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsDunsirn, M.M. / Bockhaus, N.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 the Enzymes Required for the Production of 2,3,4-triacetoamido-2,3,4-trideoxy-l-arabinose in Psychrobacter cryohalolentis K5
Authors: Bockhaus, N.J. / Dunsirn, M.M. / Thoden, J.B. / Holden, H.M.
History
DepositionJan 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 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: Acetyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1322
Polymers19,5991
Non-polymers1,5331
Water1,11762
1
A: Acetyltransferase, putative
hetero molecules

A: Acetyltransferase, putative
hetero molecules

A: Acetyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3956
Polymers58,7963
Non-polymers4,5993
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445z-1/2,-x-1/2,-y1
crystal symmetry operation12_455-y-1/2,-z,x+1/21
Buried area12390 Å2
ΔGint-68 kcal/mol
Surface area20240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.903, 114.903, 114.903
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-346-

HOH

21A-357-

HOH

31A-358-

HOH

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Components

#1: Protein Acetyltransferase, putative


Mass: 19598.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psychrobacter cryohalolentis K5 (bacteria)
Gene: Pcryo_0619 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q1QD51
#2: Chemical ChemComp-5NG / [[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{R})-4-[[3-[2-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyldisulfanyl]ethylamino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] hydrogen phosphate / CoA-disulfide


Mass: 1533.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H70N14O32P6S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 3.24 Å3/Da / Density % sol: 62.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Protein incubated with 2 mM coenzyme A. Precipitant: 23-26% pentaerythritol ethoxylate (3/4 EO/OH), 100 mM MES (pH 6)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Aug 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 19728 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.5 % / Rsym value: 0.079 / Net I/σ(I): 52
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4.9 % / Num. unique obs: 973 / R split: 2.1 / Rsym value: 0.47 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→40.62 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.305 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24211 1017 5.2 %RANDOM
Rwork0.20242 ---
obs0.20459 18711 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.283 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.9→40.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1339 0 96 62 1497
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121462
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161401
X-RAY DIFFRACTIONr_angle_refined_deg1.491.651990
X-RAY DIFFRACTIONr_angle_other_deg0.5071.5753237
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8515176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.488510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95310245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0660.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021600
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02298
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_it4.2185.081707
X-RAY DIFFRACTIONr_mcbond_other4.2145.082707
X-RAY DIFFRACTIONr_mcangle_it5.049.083882
X-RAY DIFFRACTIONr_mcangle_other5.0389.09883
X-RAY DIFFRACTIONr_scbond_it5.7565.768755
X-RAY DIFFRACTIONr_scbond_other5.7535.77756
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.05510.4211109
X-RAY DIFFRACTIONr_long_range_B_refined9.24758.791656
X-RAY DIFFRACTIONr_long_range_B_other9.26758.91645
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.948 Å
RfactorNum. reflection% reflection
Rfree0.395 76 -
Rwork0.409 1347 -
obs--97.4 %

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