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- PDB-6zlj: Crystal Structure of UDP-Glucuronic acid 4-epimerase Y149F mutant... -

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Basic information

Entry
Database: PDB / ID: 6zlj
TitleCrystal Structure of UDP-Glucuronic acid 4-epimerase Y149F mutant from Bacillus cereus in complex with UDP-4-DEOXY-4-FLUORO-Glucuronic acid and NAD
ComponentsEpimerase domain-containing protein
KeywordsOXIDOREDUCTASE / epimerase / UDP-4-DEOXY-4-FLUORO-Glucuronic acid / NAD / UDP-sugar binding protein
Function / homologyNAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / catalytic activity / NAD(P)-binding domain superfamily / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-UGF / Epimerase domain-containing protein
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsIacovino, L.G. / Mattevi, A.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of Education Italy
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Crystallographic snapshots of UDP-glucuronic acid 4-epimerase ligand binding, rotation, and reduction.
Authors: Iacovino, L.G. / Savino, S. / Borg, A.J.E. / Binda, C. / Nidetzky, B. / Mattevi, A.
History
DepositionJun 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Epimerase domain-containing protein
B: Epimerase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5136
Polymers73,0222
Non-polymers2,4914
Water3,027168
1
A: Epimerase domain-containing protein
hetero molecules

B: Epimerase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5136
Polymers73,0222
Non-polymers2,4914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area4960 Å2
ΔGint-39 kcal/mol
Surface area23220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.199, 58.222, 64.439
Angle α, β, γ (deg.)97.250, 98.180, 109.930
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Epimerase domain-containing protein


Mass: 36510.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: IG7_05634 / Production host: Escherichia coli (E. coli) / References: UniProt: J8BY31
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-UGF / (2~{R},3~{S},4~{R},5~{R},6~{R})-6-[[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidany l)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3-fluoranyl-4,5-bis(oxidanyl)oxane-2-carboxylic acid / UDP-4-Deoxy-4-Fluoro-Glucuronic acid


Mass: 582.276 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H21FN2O17P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 1.98 Å3/Da / Density % sol: 37.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 200 mM potassium acetate, 14-24% PEG3350, 2 mM NAD, 2 mM UDP-4-FLUORO-4-DEOXY-Glucuronic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→45.25 Å / Num. obs: 54213 / % possible obs: 93 % / Redundancy: 9.1 % / CC1/2: 0.99 / Net I/σ(I): 8.4
Reflection shellResolution: 1.7→1.74 Å / Num. unique obs: 3953 / CC1/2: 0.69

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U4Q

5u4q


Resolution: 1.7→45.25 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.132 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2154 2808 4.9 %RANDOM
Rwork0.1725 ---
obs0.1746 54213 92.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.05 Å2 / Biso mean: 29.357 Å2 / Biso min: 18.12 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å2-0.8 Å2-1 Å2
2---0.86 Å20.92 Å2
3---2.56 Å2
Refinement stepCycle: final / Resolution: 1.7→45.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4930 0 162 168 5260
Biso mean--27.51 36.07 -
Num. residues----628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135210
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174846
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.6647090
X-RAY DIFFRACTIONr_angle_other_deg1.381.58711298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7815626
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32123.393224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58715900
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.681518
X-RAY DIFFRACTIONr_chiral_restr0.0820.2730
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025620
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021000
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 199 -
Rwork0.296 3953 -
all-4152 -
obs--91.21 %

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