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- PDB-4xgk: Crystal structure of UDP-galactopyranose mutase from Corynebacter... -

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Basic information

Entry
Database: PDB / ID: 4xgk
TitleCrystal structure of UDP-galactopyranose mutase from Corynebacterium diphtheriae in complex with 2-[4-(4-chlorophenyl)-7-(2-thienyl)-2-thia-5,6,8,9-tetrazabicyclo[4.3.0]nona-4,7,9-trien-3-yl]acetic
ComponentsUDP-galactopyranose mutase
KeywordsISOMERASE/ISOMERASE INHIBITOR / UDP-galactopyranose mutase / Corynebacterium diphtheriae / inhibitor / galactofuranose / ISOMERASE-ISOMERASE INHIBITOR complex
Function / homology
Function and homology information


UDP-galactopyranose mutase / UDP-galactopyranose mutase activity / nucleotide binding
Similarity search - Function
UDP-galactopyranose mutase / UDP-galactopyranose mutase, C-terminal / UDP-galactopyranose mutase / NAD(P)-binding Rossmann-like domain / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-40K / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / UDP-galactopyranose mutase
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.652 Å
AuthorsWangkanont, K. / Heroux, A. / Forest, K.T. / Kiessling, L.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01_AI063596 United States
CitationJournal: Acs Chem.Biol. / Year: 2015
Title: Virtual Screening for UDP-Galactopyranose Mutase Ligands Identifies a New Class of Antimycobacterial Agents.
Authors: Kincaid, V.A. / London, N. / Wangkanont, K. / Wesener, D.A. / Marcus, S.A. / Heroux, A. / Nedyalkova, L. / Talaat, A.M. / Forest, K.T. / Shoichet, B.K. / Kiessling, L.L.
History
DepositionDec 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 9, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.5Sep 27, 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
B: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,34517
Polymers89,9322
Non-polymers3,41415
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)179.362, 179.362, 145.236
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein UDP-galactopyranose mutase /


Mass: 44965.848 Da / Num. of mol.: 2 / Fragment: UNP residues 18-404
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Strain: ATCC 700971 / NCTC 13129 / Biotype gravis / Gene: glf, DIP2203 / Plasmid: pMAL c5x
Details (production host): maltose binding protein in pMAL c5x was removed and replaced with His-tagged UDP-galactopyranose mutase
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6NER4, UDP-galactopyranose mutase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-40K / [(7S)-6-(4-chlorophenyl)-3-(thiophen-2-yl)-7H-[1,2,4]triazolo[3,4-b][1,3,4]thiadiazin-7-yl]acetic acid


Mass: 390.867 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H11ClN4O2S2
#4: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 3.75 Å3/Da / Density % sol: 67.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100 mM Bis-Tris, 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 40032 / % possible obs: 99.2 % / Redundancy: 9.8 % / Biso Wilson estimate: 75.43 Å2 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.025 / Rrim(I) all: 0.08 / Χ2: 0.779 / Net I/av σ(I): 25.888 / Net I/σ(I): 7.9 / Num. measured all: 391794
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.65-2.749.70.7938950.8180.2650.8340.49598.6
2.74-2.8510.10.53639140.9230.1750.5640.51698.9
2.85-2.989.70.36439360.9560.1220.3840.55599
2.98-3.1410.20.24239330.9820.0780.2540.61599.1
3.14-3.349.70.15839570.990.0530.1670.76199.1
3.34-3.6100.10839750.9950.0360.1140.999.3
3.6-3.969.90.08739800.9960.0290.0921.05699.4
3.96-4.539.70.0740440.9970.0240.0741.09199.6
4.53-5.719.80.06340890.9980.0210.0660.98999.7
5.71-509.10.04643090.9990.0160.0490.899.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I8T

1i8t


Resolution: 2.652→48.771 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2269 3750 4.98 %
Rwork0.1821 71520 -
obs0.1844 75270 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 151.4 Å2 / Biso mean: 77.254 Å2 / Biso min: 42.31 Å2
Refinement stepCycle: final / Resolution: 2.652→48.771 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6332 0 211 34 6577
Biso mean--98.93 62.82 -
Num. residues----772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096761
X-RAY DIFFRACTIONf_angle_d1.39201
X-RAY DIFFRACTIONf_chiral_restr0.049914
X-RAY DIFFRACTIONf_plane_restr0.0081198
X-RAY DIFFRACTIONf_dihedral_angle_d16.8852469
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.652-2.74680.39083640.30737049741398
2.7468-2.85670.34083790.28717122750199
2.8567-2.98670.3573720.28167138751099
2.9867-3.14420.29313800.25167164754499
3.1442-3.34110.29383730.2417156752999
3.3411-3.5990.27983810.21471467527100
3.599-3.96110.23623750.187171497524100
3.9611-4.53390.1873740.139972037577100
4.5339-5.71080.18693740.145871967570100
5.7108-48.7790.18023780.153471977575100

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