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- PDB-6zl6: Crystal Structure of UDP-Glucuronic acid 4-epimerase from Bacillu... -

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Basic information

Entry
Database: PDB / ID: 6zl6
TitleCrystal Structure of UDP-Glucuronic acid 4-epimerase from Bacillus cereus in complex with UDP and NAD
ComponentsEpimerase domain-containing protein
KeywordsOXIDOREDUCTASE / epimerase / UDP / 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 / Epimerase domain-containing protein
Function and homology information
Biological speciesBacillus cereus HuA2-4 (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)75,1896
Polymers73,0542
Non-polymers2,1354
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-55 kcal/mol
Surface area23460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.482, 58.560, 64.904
Angle α, β, γ (deg.)96.770, 98.410, 110.300
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-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.02 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 200 mM potassium acetate and 14-24% PEG 3350, 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: 1.7→45.35 Å / Num. obs: 55496 / % possible obs: 93 % / Redundancy: 1.7 % / CC1/2: 0.99 / Net I/σ(I): 10.2
Reflection shellResolution: 1.7→1.74 Å / Num. unique obs: 4023 / CC1/2: 0.88

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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→45.35 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.648 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2025 2872 4.9 %RANDOM
Rwork0.1707 ---
obs0.1722 55496 92.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.86 Å2 / Biso mean: 25.573 Å2 / Biso min: 13.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20.42 Å2-0.34 Å2
2--0.2 Å20.82 Å2
3----0.54 Å2
Refinement stepCycle: final / Resolution: 1.7→45.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4932 0 138 251 5321
Biso mean--21.58 32.78 -
Num. residues----628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135186
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174834
X-RAY DIFFRACTIONr_angle_refined_deg1.6751.6567054
X-RAY DIFFRACTIONr_angle_other_deg1.4151.5811264
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9085626
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.12523.393224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82815900
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5851518
X-RAY DIFFRACTIONr_chiral_restr0.0820.2716
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025614
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02998
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 210 -
Rwork0.288 4023 -
all-4233 -
obs--90.95 %

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