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- PDB-8vr7: crystal structure of the Pcryo_0619 N-acetyltransferase from Psyc... -

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Basic information

Entry
Database: PDB / ID: 8vr7
Titlecrystal structure of the Pcryo_0619 N-acetyltransferase from Psychrobacter cryohalolentis K5 int he presence of acetyl coenzyme A
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
ACETYL COENZYME *A / COENZYME A / Chem-EP1 / 3'-PHOSPHATE-ADENOSINE-5'-DIPHOSPHATE / Acetyltransferase, putative
Similarity search - Component
Biological speciesPsychrobacter cryohalolentis K5 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 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
B: Acetyltransferase, putative
C: Acetyltransferase, putative
D: Acetyltransferase, putative
E: Acetyltransferase, putative
F: Acetyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,24816
Polymers117,5916
Non-polymers5,65710
Water12,106672
1
A: Acetyltransferase, putative
B: Acetyltransferase, putative
C: Acetyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4978
Polymers58,7963
Non-polymers2,7015
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12640 Å2
ΔGint-59 kcal/mol
Surface area20220 Å2
MethodPISA
2
D: Acetyltransferase, putative
E: Acetyltransferase, putative
F: Acetyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7528
Polymers58,7963
Non-polymers2,9565
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12830 Å2
ΔGint-66 kcal/mol
Surface area22310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.895, 157.818, 66.046
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-335-

HOH

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Acetyltransferase, putative


Mass: 19598.547 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psychrobacter cryohalolentis K5 (bacteria)
Strain: Pcryo_0619 / Gene: Pcryo_0619 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q1QD51

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Non-polymers , 6 types, 682 molecules

#2: Chemical
ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-EP1 / 3-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]PROPANE-1-SULFONIC ACID


Mass: 252.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-PAP / 3'-PHOSPHATE-ADENOSINE-5'-DIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 672 / 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: 2.39 Å3/Da / Density % sol: 48.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Protein incubated with 3 mM acetyl-CoA. Precipitant: 8-12% PEG 8000 and 100 mM homopipes (pH 5)

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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: Nov 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 89307 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.5 % / Rsym value: 0.084 / Net I/σ(I): 14.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 12536 / Rsym value: 0.4 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→29.69 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.91 / SU B: 4.632 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23993 4466 5 %RANDOM
Rwork0.19733 ---
obs0.19948 84841 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.034 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.9→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8064 0 355 672 9091
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0128668
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168437
X-RAY DIFFRACTIONr_angle_refined_deg1.3661.64511765
X-RAY DIFFRACTIONr_angle_other_deg0.4491.57519509
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.67151089
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.503551
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.192101516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.060.21367
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029671
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021808
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_it1.4711.6874288
X-RAY DIFFRACTIONr_mcbond_other1.4691.6874288
X-RAY DIFFRACTIONr_mcangle_it2.3583.0165352
X-RAY DIFFRACTIONr_mcangle_other2.3583.0175353
X-RAY DIFFRACTIONr_scbond_it2.3382.1084380
X-RAY DIFFRACTIONr_scbond_other2.3382.1094381
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7973.7316399
X-RAY DIFFRACTIONr_long_range_B_refined5.25918.3910136
X-RAY DIFFRACTIONr_long_range_B_other5.25918.3910137
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 334 -
Rwork0.343 6118 -
obs--98.96 %

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