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

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Basic information

Entry
Database: PDB / ID: 6zla
TitleCrystal Structure of UDP-Glucuronic acid 4-epimerase from Bacillus cereus in complex with NAD
ComponentsEpimerase domain-containing protein
KeywordsOXIDOREDUCTASE / epimerase / NAD / UDP-sugar binding protein
Function / homology
Function and homology information


NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Epimerase domain-containing protein
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
C: Epimerase domain-containing protein
D: Epimerase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,7628
Polymers146,1084
Non-polymers2,6544
Water4,324240
1
A: Epimerase domain-containing protein
B: Epimerase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3814
Polymers73,0542
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-37 kcal/mol
Surface area24810 Å2
MethodPISA
2
C: Epimerase domain-containing protein
hetero molecules

D: Epimerase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3814
Polymers73,0542
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555x+1/2,y+1/2,z1
Buried area4880 Å2
ΔGint-34 kcal/mol
Surface area24810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)214.503, 78.529, 87.949
Angle α, β, γ (deg.)90.000, 91.010, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Epimerase domain-containing protein


Mass: 36526.957 Da / Num. of mol.: 4
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


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.53 Å3/Da / Density % sol: 51.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8 / Details: 200 mM potassium acetate, 14-24% PEG3350, 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: 2.2→45.61 Å / Num. obs: 69067 / % possible obs: 97 % / Redundancy: 4.2 % / CC1/2: 0.99 / Net I/σ(I): 16.9
Reflection shellResolution: 2.2→2.25 Å / Num. unique obs: 4432 / CC1/2: 0.92

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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: 2.2→45.61 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.236 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.239 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2271 3576 4.9 %RANDOM
Rwork0.1784 ---
obs0.1808 69067 97.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.74 Å2 / Biso mean: 34.208 Å2 / Biso min: 17.03 Å2
Baniso -1Baniso -2Baniso -3
1--1.66 Å2-0 Å2-0.38 Å2
2---1.92 Å2-0 Å2
3---3.59 Å2
Refinement stepCycle: final / Resolution: 2.2→45.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9705 0 176 240 10121
Biso mean--23.69 35.09 -
Num. residues----1233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01310100
X-RAY DIFFRACTIONr_bond_other_d0.0020.0179474
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.63913702
X-RAY DIFFRACTIONr_angle_other_deg1.3191.57622059
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.14151221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.65623.597442
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.259151772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3891532
X-RAY DIFFRACTIONr_chiral_restr0.0730.21391
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210966
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021954
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 247 -
Rwork0.213 4432 -
all-4679 -
obs--85.76 %

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