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- PDB-8e77: rystal structure of Pcryo_0616, the aminotransferase required to ... -

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Basic information

Entry
Database: PDB / ID: 8.0E+77
Titlerystal structure of Pcryo_0616, the aminotransferase required to synthesize UDP-N-acetyl-3-amino-D-glucosaminuronic acid (UDP-GlcNAc3NA), incomplete with its external aldimine reaction intermediate
ComponentsDegT/DnrJ/EryC1/StrS aminotransferase
KeywordsTRANSFERASE / aminotransferase / Psychrobacter cryohalolentis / carbohydrate
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 / Chem-ULP / DegT/DnrJ/EryC1/StrS aminotransferase
Function and homology information
Biological speciesPsychrobacter cryohalolentis K5 (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1 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

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Structure visualization

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,28110
Polymers42,0131
Non-polymers1,2689
Water12,502694
1
A: DegT/DnrJ/EryC1/StrS aminotransferase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)86,56320
Polymers84,0272
Non-polymers2,53618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area5260 Å2
ΔGint-16 kcal/mol
Surface area25840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.708, 96.336, 139.467
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-408-

NA

21A-523-

HOH

31A-608-

HOH

41A-742-

HOH

51A-805-

HOH

61A-828-

HOH

71A-870-

HOH

81A-895-

HOH

91A-981-

HOH

101A-1150-

HOH

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Components

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


Mass: 42013.477 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-ULP / (2S,3S,4R,5R,6R)-5-(acetylamino)-6-{[(R)-{[(S)-{[(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-hydroxy-4-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}tetrahydro-2H-pyran-2-carboxylic acid (non-preferred name)


Mass: 849.479 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H34N5O22P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#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.: 694 / 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: 2.31 Å3/Da / Density % sol: 46.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Protein incubated with 5 mM UDP-GlcNAc3NA 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 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1→50 Å / Num. obs: 205549 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Rsym value: 0.051 / Net I/σ(I): 16.9
Reflection shellResolution: 1→1.1 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2 / Num. unique obs: 49306 / Rsym value: 0.456 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.27data extraction
SAINTdata reduction
SADABSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Starting model: 8.0E+75 / Resolution: 1→28.27 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.049 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.023 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1742 10539 5.1 %RANDOM
Rwork0.1462 ---
obs0.1477 195010 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.84 Å2 / Biso mean: 11.418 Å2 / Biso min: 4.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.11 Å2
Refinement stepCycle: final / Resolution: 1→28.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2776 0 81 695 3552
Biso mean--16.88 27.18 -
Num. residues----358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133077
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172819
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.6564212
X-RAY DIFFRACTIONr_angle_other_deg1.5631.576570
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2235396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11123.106161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.10215508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9881518
X-RAY DIFFRACTIONr_chiral_restr0.0890.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023502
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02611
X-RAY DIFFRACTIONr_rigid_bond_restr11.03835893
LS refinement shellResolution: 1→1.026 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 719 -
Rwork0.357 13595 -
all-14314 -
obs--93.71 %

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