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- PDB-4rpl: Crystal structure of Micobacterium tuberculosis UDP-Galactopyrano... -

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Basic information

Entry
Database: PDB / ID: 4rpl
TitleCrystal structure of Micobacterium tuberculosis UDP-Galactopyranose mutase in complex with tetrafluorinated substrate analog UDP-F4-Galp
ComponentsUDP-galactopyranose mutase
KeywordsISOMERASE / UDP-galactopyranose mutase / MtUGM / flavoenzyme / fad
Function / homology
Function and homology information


Actinobacterium-type cell wall biogenesis / UDP-galactopyranose mutase / UDP-galactopyranose mutase activity / capsule polysaccharide biosynthetic process / peptidoglycan-based cell wall / cell wall organization / flavin adenine dinucleotide binding / plasma membrane / cytosol
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-3UC / FLAVIN-ADENINE DINUCLEOTIDE / UDP-galactopyranose mutase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2499 Å
AuthorsVan Straaten, K.E. / Sanders, D.A.R.
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: Structural Basis of Ligand Binding to UDP-Galactopyranose Mutase from Mycobacterium tuberculosis Using Substrate and Tetrafluorinated Substrate Analogues.
Authors: van Straaten, K.E. / Kuttiyatveetil, J.R. / Sevrain, C.M. / Villaume, S.A. / Jimenez-Barbero, J. / Linclau, B. / Vincent, S.P. / Sanders, D.A.
History
DepositionOct 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Feb 11, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Refinement description / Category: pdbx_database_related / software / Item: _pdbx_database_related.db_id / _software.name
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: UDP-galactopyranose mutase
A: UDP-galactopyranose mutase
C: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,9609
Polymers137,7853
Non-polymers4,1756
Water7,584421
1
B: UDP-galactopyranose mutase
hetero molecules

B: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6406
Polymers91,8572
Non-polymers2,7844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area4950 Å2
ΔGint-22 kcal/mol
Surface area31000 Å2
MethodPISA
2
A: UDP-galactopyranose mutase
C: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6406
Polymers91,8572
Non-polymers2,7844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-20 kcal/mol
Surface area31740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.290, 98.290, 100.520
Angle α, β, γ (deg.)90.00, 109.94, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein UDP-galactopyranose mutase / UGM / UDP-GALP mutase / Uridine 5-diphosphate galactopyranose mutase


Mass: 45928.348 Da / Num. of mol.: 3 / Mutation: P306R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: glf, glfA, Rv3809c / Plasmid: pDEST-His-MBP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: P9WIQ1, UDP-galactopyranose mutase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-3UC / [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,5S,6R)-3,3,4,4-tetrafluoro-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)


Mass: 606.265 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H20F4N2O15P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.89 Å3/Da / Density % sol: 57.39 %
Crystal growTemperature: 277 K / Method: hanging drop vapor diffusion / pH: 5.5
Details: 0.1M Bis-Tris pH 5.5, 20% PEG 3350, 10mM Hexammine cobalt (III) chloride, Hanging drop vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 8, 2014
RadiationMonochromator: ACCEL/BRUKER double crystal monochromator (DCM), featuring indirectly cryo-cooled first crystal and sagittally focusing second crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.2499→48.625 Å / Num. all: 74331 / Num. obs: 74331 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 43.98 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 9.39
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.2499-2.310.8741.66199.8
2.31-2.370.6842.23199.8
2.37-2.440.6372.471100
2.44-2.520.5382.92199.8
2.52-2.60.4323.6199.8
2.6-2.690.3474.42199.8
2.69-2.790.2685.58199.9
2.79-2.90.2146.8199.6
2.9-3.030.1638.48199.9
3.03-3.180.12910.34199.6
3.18-3.350.112.78199.8
3.35-3.560.07915.56199.8
3.56-3.80.06916.85199.8
3.8-4.110.06218.6199.8
4.11-4.50.05419.91199.6
4.5-5.030.05420.41199.7
5.03-5.810.05220.27199.7
5.81-7.120.04820.2199.8
7.12-10.060.04122.3199.7
10.060.0423.21198.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
MxDCdata collection
AutoProcessdata reduction
AutoProcessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MtUGM in complex with UDP-Galp (4RPG)

4rpg


Resolution: 2.2499→48.625 Å / SU ML: 0.34 / Isotropic thermal model: Isotropic / σ(F): 1.35 / Phase error: 28.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2599 3716 5 %
Rwork0.2182 --
obs0.2203 74306 99.86 %
all-74331 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.557 Å2
Refinement stepCycle: LAST / Resolution: 2.2499→48.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9564 0 273 421 10258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210300
X-RAY DIFFRACTIONf_angle_d0.59514062
X-RAY DIFFRACTIONf_dihedral_angle_d13.0123807
X-RAY DIFFRACTIONf_chiral_restr0.0241458
X-RAY DIFFRACTIONf_plane_restr0.0041811
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2499-2.28870.39331850.31923508X-RAY DIFFRACTION100
2.2887-2.33030.33091850.28423504X-RAY DIFFRACTION100
2.3303-2.37520.34821840.27713503X-RAY DIFFRACTION100
2.3752-2.42360.30171860.27853526X-RAY DIFFRACTION100
2.4236-2.47630.32841850.27763526X-RAY DIFFRACTION100
2.4763-2.53390.32871850.27253511X-RAY DIFFRACTION100
2.5339-2.59730.34771850.28033508X-RAY DIFFRACTION100
2.5973-2.66750.31441860.27263529X-RAY DIFFRACTION100
2.6675-2.7460.35121850.26273528X-RAY DIFFRACTION100
2.746-2.83460.31741840.26333493X-RAY DIFFRACTION100
2.8346-2.93590.29441860.24453530X-RAY DIFFRACTION100
2.9359-3.05350.30361850.25533515X-RAY DIFFRACTION100
3.0535-3.19240.27971860.24673536X-RAY DIFFRACTION100
3.1924-3.36070.31881850.24233508X-RAY DIFFRACTION100
3.3607-3.57120.24911860.20893541X-RAY DIFFRACTION100
3.5712-3.84680.22661860.20353523X-RAY DIFFRACTION100
3.8468-4.23370.22631870.1873551X-RAY DIFFRACTION100
4.2337-4.84590.21271860.16423548X-RAY DIFFRACTION100
4.8459-6.10340.22191880.18723572X-RAY DIFFRACTION100
6.1034-48.63670.20371910.18893630X-RAY DIFFRACTION100

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