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- PDB-6d9b: Crystal structure of Corynebacterium diphtheriae UDP-galactopyran... -

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Basic information

Entry
Database: PDB / ID: 6d9b
TitleCrystal structure of Corynebacterium diphtheriae UDP-galactopyranose mutase in complex with UDP-glucose (open, oxidized)
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 / FLAVIN-ADENINE DINUCLEOTIDE / ISOPROPYL ALCOHOL / URIDINE-5'-DIPHOSPHATE-GLUCOSE / :
Function and homology information
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 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)47,3538
Polymers45,7381
Non-polymers1,6157
Water3,999222
1
A: UDP-galactopyranose mutase
hetero molecules

A: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,70616
Polymers91,4752
Non-polymers3,23014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Unit cell
Length a, b, c (Å)98.060, 98.060, 127.150
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, 229 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#5: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 63.19 %
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-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 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: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.2→38.83 Å / Num. obs: 60110 / % possible obs: 100 % / Redundancy: 28.1 % / Biso Wilson estimate: 39.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.022 / Rrim(I) all: 0.119 / Net I/σ(I): 19.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.2-2.2727.30.89529070.910.1730.912100
8.8-38.8322.90.0435910.9990.0090.04498.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.43 Å38.83 Å
Translation7.43 Å38.83 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: 2.2→38.825 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.05
RfactorNum. reflection% reflection
Rfree0.1917 1591 4.95 %
Rwork0.1534 --
obs0.1554 60110 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.91 Å2 / Biso mean: 42.7116 Å2 / Biso min: 25.11 Å2
Refinement stepCycle: final / Resolution: 2.2→38.825 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3165 0 106 222 3493
Biso mean--46.5 44.77 -
Num. residues----386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083378
X-RAY DIFFRACTIONf_angle_d1.1164594
X-RAY DIFFRACTIONf_chiral_restr0.043465
X-RAY DIFFRACTIONf_plane_restr0.004641
X-RAY DIFFRACTIONf_dihedral_angle_d13.6741272
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
2.2-2.27870.2383210.200257126033
2.2787-2.36990.25592940.194556815975
2.3699-2.47770.24242780.18957446022
2.4777-2.60830.20772940.173857186012
2.6083-2.77170.23183290.179556906019
2.7717-2.98560.26162620.187457476009
2.9856-3.2860.22912900.172557386028
3.286-3.76110.17992730.151157255998
3.7611-4.73730.16513280.122656746002
4.7373-38.83110.14453060.127957066012

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