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- PDB-8e75: Crystal structure of Pcryo_0616, the aminotransferase required to... -

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Basic information

Entry
Database: PDB / ID: 8.0E+75
TitleCrystal structure of Pcryo_0616, the aminotransferase required to synthesize UDP-N-acetyl-3-amino-D-glucosaminuronic acid (UDP-GlcNAc3NA)
ComponentsDegT/DnrJ/EryC1/StrS aminotransferase
KeywordsTRANSFERASE / aminotransferase / Psychrobacter cryohalolentis / carbohydratae
Function / homologyDegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / transaminase activity / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / DegT/DnrJ/EryC1/StrS aminotransferase
Function and homology information
Biological speciesPsychrobacter cryohalolentis K5 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsHofmeister, D.L. / Seltzner, C.A. / 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: 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 23, 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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DegT/DnrJ/EryC1/StrS aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4585
Polymers42,2491
Non-polymers2094
Water12,376687
1
A: DegT/DnrJ/EryC1/StrS aminotransferase
hetero molecules

A: DegT/DnrJ/EryC1/StrS aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,91510
Polymers84,4972
Non-polymers4188
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area5700 Å2
ΔGint-11 kcal/mol
Surface area25720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.828, 96.344, 139.658
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-401-

NA

21A-623-

HOH

31A-680-

HOH

41A-687-

HOH

51A-788-

HOH

61A-826-

HOH

71A-868-

HOH

81A-922-

HOH

91A-960-

HOH

101A-984-

HOH

111A-1147-

HOH

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Components

#1: Protein DegT/DnrJ/EryC1/StrS aminotransferase / UDP-N-acetyl-3-amino-glucuronic acid transaminase


Mass: 42248.543 Da / Num. of mol.: 1
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_0616 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q1QD54
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 687 / 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: 2.3 Å3/Da / Density % sol: 46.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Protein incubated with 5 mM UDP and 1 mM PLP. Precipitant: 18 - 22% poly(ethylene glycol) 8000, 200 mM LiCl, and 100 mM HEPPS (pH 8.0)

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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: Mar 2, 2019
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: 106460 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Rsym value: 0.051 / Net I/σ(I): 19.5
Reflection shellResolution: 1.25→1.35 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 21148 / Rsym value: 0.42 / % possible all: 91.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.27data extraction
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3nyu

3nyu


Resolution: 1.25→28.93 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.738 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1704 5362 5 %RANDOM
Rwork0.154 ---
obs0.1548 101098 97.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.88 Å2 / Biso mean: 10.402 Å2 / Biso min: 3.81 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.25→28.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2791 0 13 692 3496
Biso mean--21.83 24.4 -
Num. residues----358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132963
X-RAY DIFFRACTIONr_bond_other_d00.0172728
X-RAY DIFFRACTIONr_angle_refined_deg1.7761.6484053
X-RAY DIFFRACTIONr_angle_other_deg1.581.5686360
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2495388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39923.618152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.46515492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.211515
X-RAY DIFFRACTIONr_chiral_restr0.2430.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023370
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02578
LS refinement shellResolution: 1.25→1.278 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.305 358 -
Rwork0.31 6168 -
obs--81.96 %

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