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- PDB-9cm8: UDP-GlcNAc 2-epimerase MnaA of Paenibacillus alvei -

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Basic information

Entry
Database: PDB / ID: 9cm8
TitleUDP-GlcNAc 2-epimerase MnaA of Paenibacillus alvei
ComponentsUDP-N-acetylglucosamine 2-epimerase (non-hydrolyzing)
KeywordsISOMERASE / Epimerase / UDP-GlcNAc / UDP-ManNAc / SUGAR BINDING PROTEIN
Function / homologyDI(HYDROXYETHYL)ETHER / :
Function and homology information
Biological speciesPaenibacillus alvei (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLegg, M.S.G. / Mateyko, N. / Evans, S.V.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Front Mol Biosci / Year: 2024
Title: Insights into structure and activity of a UDP-GlcNAc 2-epimerase involved in secondary cell wall polymer biosynthesis in Paenibacillus alvei.
Authors: Stefanovic, C. / Legg, M.S.G. / Mateyko, N. / Ender, J.J. / Kuvek, T. / Oostenbrink, C. / Schaffer, C. / Evans, S.V. / Hager-Mair, F.F.
History
DepositionJul 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Database references / Structure summary / Category: citation / pdbx_entry_details
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-N-acetylglucosamine 2-epimerase (non-hydrolyzing)
B: UDP-N-acetylglucosamine 2-epimerase (non-hydrolyzing)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1334
Polymers88,9212
Non-polymers2122
Water3,297183
1
A: UDP-N-acetylglucosamine 2-epimerase (non-hydrolyzing)
hetero molecules

B: UDP-N-acetylglucosamine 2-epimerase (non-hydrolyzing)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1334
Polymers88,9212
Non-polymers2122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_444-x-1,y-1/2,-z-11
Buried area3150 Å2
ΔGint-14 kcal/mol
Surface area29370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.816, 81.763, 107.722
Angle α, β, γ (deg.)90.00, 97.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UDP-N-acetylglucosamine 2-epimerase (non-hydrolyzing)


Mass: 44460.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus alvei (bacteria) / Strain: CCM 2051T / Gene: GQA12_18035 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A8I2FAI9, UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing)
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
22.2545.37
1
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 0.16 M CaCl2, 0.1 M Tris/HCl pH 8.8, and 15% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jan 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 39705 / % possible obs: 99 % / Redundancy: 4 % / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.031 / Rrim(I) all: 0.065 / Χ2: 0.938 / Net I/σ(I): 17.5 / Num. measured all: 160170
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.2-2.2830.21136620.9570.9890.1330.2510.9991.4
2.28-2.373.70.18839290.9730.9930.1070.2170.98799.3
2.37-2.4840.1639960.9820.9950.0880.1830.973100
2.48-2.614.10.1340060.9890.9970.070.1490.928100
2.61-2.774.30.10539920.9930.9980.0550.1190.933100
2.77-2.994.40.08439870.9940.9980.0440.0950.95100
2.99-3.293.90.06640250.9940.9980.0380.0760.94199.9
3.29-3.764.40.05340010.9970.9990.0270.060.892100
3.76-4.744.40.04240230.9980.9990.0220.0470.93499.7
4.74-504.10.03540840.99910.0190.040.89299.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.118 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.303 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26327 2017 5.1 %RANDOM
Rwork0.20979 ---
obs0.2125 37651 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.542 Å2
Baniso -1Baniso -2Baniso -3
1--1.97 Å20 Å2-1.29 Å2
2--3.83 Å20 Å2
3----1.49 Å2
Refinement stepCycle: 1 / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5646 0 14 183 5843
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135801
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175338
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.6417919
X-RAY DIFFRACTIONr_angle_other_deg1.3011.5712319
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4045739
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.66922.321280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.30515890
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0341533
X-RAY DIFFRACTIONr_chiral_restr0.0850.2791
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026513
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021166
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.853.4562962
X-RAY DIFFRACTIONr_mcbond_other2.8463.4552961
X-RAY DIFFRACTIONr_mcangle_it4.3355.173693
X-RAY DIFFRACTIONr_mcangle_other4.3355.173694
X-RAY DIFFRACTIONr_scbond_it3.1413.7072839
X-RAY DIFFRACTIONr_scbond_other3.143.7072840
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9625.454225
X-RAY DIFFRACTIONr_long_range_B_refined7.06540.8356197
X-RAY DIFFRACTIONr_long_range_B_other7.0640.8196186
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.203→2.261 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 157 -
Rwork0.261 2575 -
obs--93.18 %

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