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- PDB-6zld: Crystal Structure of UDP-Glucuronic acid 4-epimerase from Bacillu... -

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Basic information

Entry
Database: PDB / ID: 6zld
TitleCrystal Structure of UDP-Glucuronic acid 4-epimerase from Bacillus cereus in complex with UDP-Glucuronic acid and NAD
ComponentsEpimerase domain-containing protein
KeywordsOXIDOREDUCTASE / epimerase / UDP-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 / URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID / Epimerase domain-containing protein
Function and homology information
Biological speciesBacillus cereus HuA2-4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsIacovino, L.G. / Savino, S. / 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)75,5416
Polymers73,0542
Non-polymers2,4874
Water5,368298
1
A: Epimerase domain-containing protein
hetero molecules

B: Epimerase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5416
Polymers73,0542
Non-polymers2,4874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area6940 Å2
ΔGint-51 kcal/mol
Surface area23190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.364, 58.446, 64.734
Angle α, β, γ (deg.)96.800, 98.360, 110.620
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Epimerase domain-containing protein


Mass: 36526.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus HuA2-4 (bacteria) / Gene: IG7_05634 / Production host: Escherichia coli (E. coli) / References: UniProt: J8BY31
#2: Chemical ChemComp-NAD / 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-UGA / URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID / UDP-GLUCURONIC ACID


Mass: 580.285 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N2O18P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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 Å3/Da / Density % sol: 38.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 200 mM potassium acetate and 14-24% PEG3350, 2 mM UDP-glucuronic acid, 2 mM NAD+

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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: 1.8→45.22 Å / Num. obs: 49095 / % possible obs: 95 % / Redundancy: 1.6 % / CC1/2: 0.99 / Net I/σ(I): 9.3
Reflection shellResolution: 1.8→1.84 Å / Num. unique obs: 3399 / CC1/2: 0.78

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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: 1.8→45.22 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.085 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2075 2398 4.9 %RANDOM
Rwork0.1679 ---
obs0.1698 46695 93.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.39 Å2 / Biso mean: 22.478 Å2 / Biso min: 10.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å2-0.35 Å2-0.71 Å2
2--0.12 Å20.48 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 1.8→45.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4932 0 162 298 5392
Biso mean--17.39 29.82 -
Num. residues----628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135212
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174844
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.6467094
X-RAY DIFFRACTIONr_angle_other_deg1.3731.57411294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1515626
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.16223.393224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95615900
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2171518
X-RAY DIFFRACTIONr_chiral_restr0.0790.2730
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025622
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02998
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 189 -
Rwork0.246 3399 -
all-3588 -
obs--92.09 %

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