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- PDB-8e62: STRUCTURE OF Pcryo_0615 from Psychrobacter cryohalolentis, an N-a... -

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Basic information

Entry
Database: PDB / ID: 8.0E+62
TitleSTRUCTURE OF Pcryo_0615 from Psychrobacter cryohalolentis, an N-acetyltransferase required to produce Diacetamido-2,3-dideoxy-D-glucuronic acid
ComponentsUDP-N-acetylglucosamine acyltransferase
KeywordsTRANSFERASE / N-acetyltransferase / 2 / 3-diacetamido-2 / 3-dideoxy-D-glucuronic acid / Psychrobacter cryohalolentis
Function / homologyacyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase activity / Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / lipid A biosynthetic process / Trimeric LpxA-like superfamily / COENZYME A / Chem-MJZ / UDP-N-acetylglucosamine acyltransferase
Function and homology information
Biological speciesPsychrobacter cryohalolentis K5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHofmeister, D.L. / Bockhaus, N.J. / Seltzner, C.A. / 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: Protein Sci. / Year: 2023
Title: Investigation of the enzymes required for the biosynthesis of 2,3-diacetamido-2,3-dideoxy-d-glucuronic acid in Psychrobacter cryohalolentis K5 T.
Authors: Hofmeister, D.L. / Seltzner, C.A. / Bockhaus, N.J. / Thoden, J.B. / Holden, H.M.
History
DepositionAug 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.title / _citation.year
Revision 1.2Oct 25, 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
A: UDP-N-acetylglucosamine acyltransferase
B: UDP-N-acetylglucosamine acyltransferase
C: UDP-N-acetylglucosamine acyltransferase
D: UDP-N-acetylglucosamine acyltransferase
E: UDP-N-acetylglucosamine acyltransferase
F: UDP-N-acetylglucosamine acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,61217
Polymers123,1006
Non-polymers6,51211
Water11,367631
1
A: UDP-N-acetylglucosamine acyltransferase
B: UDP-N-acetylglucosamine acyltransferase
C: UDP-N-acetylglucosamine acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1169
Polymers61,5503
Non-polymers3,5666
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-61 kcal/mol
Surface area21070 Å2
MethodPISA
2
D: UDP-N-acetylglucosamine acyltransferase
E: UDP-N-acetylglucosamine acyltransferase
F: UDP-N-acetylglucosamine acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4968
Polymers61,5503
Non-polymers2,9465
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-62 kcal/mol
Surface area20810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.113, 79.768, 96.616
Angle α, β, γ (deg.)90.000, 114.280, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
UDP-N-acetylglucosamine acyltransferase


Mass: 20516.600 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psychrobacter cryohalolentis K5 (bacteria)
Strain: ATCC BAA-1226 / DSM 17306 / VKM B-2378 / K5 / Gene: Pcryo_0615 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q1QD55
#2: Chemical ChemComp-MJZ / (2S,3S,4R,5R,6R)-5-(acetylamino)-4-amino-6-{[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-3-hydroxytetrahydro-2H-pyran-2-carboxylic acid


Mass: 620.352 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H26N4O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 631 / 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: 2.41 Å3/Da / Density % sol: 48.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Protein incubated with: 5 mM CoA and 5 mM UDP-GlcNAc3NA. Precipitant: 16 - 20% PEG-3350, 2% 2-methyl-2,4-pentanediol, and 100 mM MES (pH 6.0)

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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 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 102909 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rsym value: 0.079 / Net I/σ(I): 30.8
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 5.3 / Num. unique obs: 5043 / Rsym value: 0.226 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5dem

5dem


Resolution: 1.8→48.15 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.297 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2081 5027 4.9 %RANDOM
Rwork0.1659 ---
obs0.168 97882 98.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 114.05 Å2 / Biso mean: 22.1 Å2 / Biso min: 9.31 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.8→48.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8172 0 410 631 9213
Biso mean--38.08 30.46 -
Num. residues----1082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0138859
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178088
X-RAY DIFFRACTIONr_angle_refined_deg1.5571.64612108
X-RAY DIFFRACTIONr_angle_other_deg1.3251.57218886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3551107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6624.387367
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.932151427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0711514
X-RAY DIFFRACTIONr_chiral_restr0.0760.21269
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029680
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021568
LS refinement shellResolution: 1.802→1.849 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 377 -
Rwork0.191 7032 -
all-7409 -
obs--95.49 %

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