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- PDB-6d9a: Crystal structure of Corynebacterium diphtheriae UDP-galactopyran... -

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Basic information

Entry
Database: PDB / ID: 6d9a
TitleCrystal structure of Corynebacterium diphtheriae UDP-galactopyranose mutase in complex with UDP-GalNAc (open, reduced)
ComponentsUDP-galactopyranose mutase
KeywordsISOMERASE / galatofuranose / galactopyranose / galactose / UDP / enzyme / UDP-galactopyranose mutase
Function / homologyNAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / ISOPROPYL ALCOHOL / URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE / :
Function and homology information
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsWangkanont, K. / Kiessling, L.L. / Forest, K.T.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI063596 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI126592 United States
National Science Foundation (NSF, United States)IOS1353674 United States
CitationJournal: To be published
Title: Substrate recognition by FAD in UDP-galactopyranose mutase
Authors: Wangkanont, K. / Forest, K.T. / Kiessling, L.L.
History
DepositionApr 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: 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: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2165
Polymers45,7381
Non-polymers1,4784
Water32418
1
A: UDP-galactopyranose mutase
hetero molecules

A: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,43110
Polymers91,4752
Non-polymers2,9568
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Unit cell
Length a, b, c (Å)97.430, 97.430, 128.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein UDP-galactopyranose mutase


Mass: 45737.668 Da / Num. of mol.: 1 / Fragment: UDP-galactopyranose mutase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Gene: BU167_07490 / Plasmid: modified pMAL C5x / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A246CDW5

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Non-polymers , 5 types, 22 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#4: Chemical ChemComp-UD2 / URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE / (2R,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate


Mass: 607.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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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: 3.34 Å3/Da / Density % sol: 63.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 mM Tris, 28% PEG400, 20% isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 13, 2014
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.9→48.72 Å / Num. obs: 26212 / % possible obs: 100 % / Redundancy: 27.8 % / Biso Wilson estimate: 69.02 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.023 / Rrim(I) all: 0.123 / Net I/σ(I): 22.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.9-3.0827.80.8822540.9380.1670.895100
8.7-48.7223.50.0416170.9990.0090.04299.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.42 Å47.01 Å
Translation7.42 Å47.01 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.3.11data scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BR7

5br7


Resolution: 2.9→47.009 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.12
RfactorNum. reflection% reflection
Rfree0.2326 738 5.2 %
Rwork0.1653 --
obs0.1688 26212 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.39 Å2 / Biso mean: 63.0951 Å2 / Biso min: 27.81 Å2
Refinement stepCycle: final / Resolution: 2.9→47.009 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3165 0 97 18 3280
Biso mean--66.68 49.86 -
Num. residues----386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013371
X-RAY DIFFRACTIONf_angle_d1.234582
X-RAY DIFFRACTIONf_chiral_restr0.05464
X-RAY DIFFRACTIONf_plane_restr0.005634
X-RAY DIFFRACTIONf_dihedral_angle_d14.6121271
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.9001-3.00370.32031480.24324622610
3.0037-3.12390.32061290.239825102639
3.1239-3.26610.33131070.231125042611
3.2661-3.43820.34311340.198824892623
3.4382-3.65360.29531450.196124732618
3.6536-3.93550.26691750.184924582633
3.9355-4.33130.1981290.14224742603
4.3313-4.95750.17281330.128925032636
4.9575-6.24360.2041260.145824852611
6.2436-47.01510.17721370.139924912628

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