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- PDB-7l7z: x-ray structure of the N-acetyltransferase Pcryo_0637 from psychr... -

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Basic information

Entry
Database: PDB / ID: 7l7z
Titlex-ray structure of the N-acetyltransferase Pcryo_0637 from psychrobacter cryohalolentis in the presence of coenzyme A and UDP-di-N-acetyl-bacillosamine
ComponentsPutative acetyl transferase protein
KeywordsTRANSFERASE / beta helix / bacillosamine / lipopolysaccharide / carbohydrate
Function / homologySialic acid O-acyltransferase NeuD-like / PglD, N-terminal / PglD N-terminal domain / Trimeric LpxA-like superfamily / transferase activity / COENZYME A / UDP-di-N-acetyl-alpha-bacillosamine / Acetyl transferase protein
Function and homology information
Biological speciesPsychrobacter cryohalolentis (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.55 Å
AuthorsLinehan, M.P. / 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)GM134643 United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Characterization of two enzymes from Psychrobacter cryohalolentis that are required for the biosynthesis of an unusual diacetamido-d-sugar.
Authors: Linehan, M.P. / Thoden, J.B. / Holden, H.M.
History
DepositionDec 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Category: citation / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Putative acetyl transferase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7069
Polymers23,6801
Non-polymers2,0268
Water4,053225
1
AAA: Putative acetyl transferase protein
hetero molecules

AAA: Putative acetyl transferase protein
hetero molecules

AAA: Putative acetyl transferase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,11927
Polymers71,0413
Non-polymers6,07924
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area13510 Å2
ΔGint-150 kcal/mol
Surface area23220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.898, 96.898, 66.630
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11AAA-303-

CL

21AAA-307-

MPD

31AAA-591-

HOH

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein Putative acetyl transferase protein


Mass: 23680.221 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psychrobacter cryohalolentis (strain ATCC BAA-1226 / DSM 17306 / VKM B-2378 / K5) (bacteria)
Strain: ATCC BAA-1226 / DSM 17306 / VKM B-2378 / K5 / Gene: Pcryo_0637 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1QD33

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Non-polymers , 5 types, 233 molecules

#2: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-XQA / UDP-di-N-acetyl-alpha-bacillosamine


Mass: 632.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H30N4O16P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 23-26% MPD, 100 mM HEPES. protein incubated with 5 mM coenzyme A and 20 mM UDP-2,4-diacetamido-2,4,6-trideoxy-D-glucose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54718 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Sep 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54718 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 33312 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rsym value: 0.045 / Net I/σ(I): 19.6
Reflection shellResolution: 1.55→1.65 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 3 / Num. unique obs: 5566 / Rsym value: 0.341 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7l7y

7l7y


Resolution: 1.55→30.983 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.614 / SU ML: 0.055 / Cross valid method: FREE R-VALUE / ESU R: 0.075 / ESU R Free: 0.076
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1903 1712 5.139 %
Rwork0.162 31600 -
all0.164 --
obs-33312 98.124 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.657 Å2
Baniso -1Baniso -2Baniso -3
1-0.228 Å20.114 Å20 Å2
2--0.228 Å20 Å2
3----0.739 Å2
Refinement stepCycle: LAST / Resolution: 1.55→30.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1612 0 130 225 1967
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131796
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171710
X-RAY DIFFRACTIONr_angle_refined_deg1.6341.6812465
X-RAY DIFFRACTIONr_angle_other_deg1.3671.5993960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9715227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.10823.71470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74415281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.082155
X-RAY DIFFRACTIONr_chiral_restr0.0660.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021935
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02329
X-RAY DIFFRACTIONr_nbd_refined0.2030.2342
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.21638
X-RAY DIFFRACTIONr_nbtor_refined0.1610.2889
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2881
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2156
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3010.226
X-RAY DIFFRACTIONr_nbd_other0.3120.295
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2610.223
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.030.21
X-RAY DIFFRACTIONr_mcbond_it1.6621.617875
X-RAY DIFFRACTIONr_mcbond_other1.6531.613874
X-RAY DIFFRACTIONr_mcangle_it2.3162.421095
X-RAY DIFFRACTIONr_mcangle_other2.3182.4241096
X-RAY DIFFRACTIONr_scbond_it2.8032.109921
X-RAY DIFFRACTIONr_scbond_other2.8022.11922
X-RAY DIFFRACTIONr_scangle_it3.9713.0581364
X-RAY DIFFRACTIONr_scangle_other3.973.0591365
X-RAY DIFFRACTIONr_lrange_it5.32122.0122015
X-RAY DIFFRACTIONr_lrange_other5.32322.0282016
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.5890.3191330.3032260X-RAY DIFFRACTION93.7696
1.589-1.6320.2581170.2682200X-RAY DIFFRACTION95.4677
1.632-1.680.2851190.2462199X-RAY DIFFRACTION97.2315
1.68-1.7310.241180.212109X-RAY DIFFRACTION97.1217
1.731-1.7880.218960.1872077X-RAY DIFFRACTION97.4003
1.788-1.8510.2181090.1832015X-RAY DIFFRACTION98.3789
1.851-1.9210.2231040.1771952X-RAY DIFFRACTION98.8462
1.921-1.9990.217760.1681928X-RAY DIFFRACTION98.8166
1.999-2.0880.193750.1531830X-RAY DIFFRACTION98.7558
2.088-2.1890.1961000.1471721X-RAY DIFFRACTION99.2371
2.189-2.3080.172820.1371683X-RAY DIFFRACTION98.8796
2.308-2.4470.1691000.1411531X-RAY DIFFRACTION99.2696
2.447-2.6160.177840.1441480X-RAY DIFFRACTION99.6178
2.616-2.8250.177890.1471331X-RAY DIFFRACTION99.5792
2.825-3.0930.194790.1341263X-RAY DIFFRACTION99.7028
3.093-3.4570.17550.1361145X-RAY DIFFRACTION99.9167
3.457-3.9890.161500.1331021X-RAY DIFFRACTION100
3.989-4.8780.124590.126835X-RAY DIFFRACTION99.8883
4.878-6.8690.21450.171664X-RAY DIFFRACTION100
6.869-30.9830.144220.169356X-RAY DIFFRACTION98.1818

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