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

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Basic information

Entry
Database: PDB / ID: 4rph
TitleCrystal structure of Micobacterium tuberculosis UDP-Galactopyranose mutase in complex with substrate UDP-Galp (reduced)
ComponentsUDP-galactopyranose mutase
KeywordsISOMERASE / UDP-galactopyranose mutase / MTUGM / flavoenzyme / FAD
Function / homology
Function and homology information


UDP-galactopyranose mutase / Actinobacterium-type cell wall biogenesis / 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
FLAVIN-ADENINE DINUCLEOTIDE / GALACTOSE-URIDINE-5'-DIPHOSPHATE / UDP-galactopyranose mutase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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)141,8419
Polymers137,7853
Non-polymers4,0566
Water2,342130
1
B: UDP-galactopyranose mutase
hetero molecules

B: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5606
Polymers91,8572
Non-polymers2,7044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
2
A: UDP-galactopyranose mutase
C: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5606
Polymers91,8572
Non-polymers2,7044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)171.730, 99.470, 100.240
Angle α, β, γ (deg.)90.000, 110.170, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain B and (resseq 5:395 )
21chain A and (resseq 5:395 )
31chain C and (resseq 5:395 )

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 5 - 395 / Label seq-ID: 5 - 395

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain B and (resseq 5:395 )BA
2chain A and (resseq 5:395 )AB
3chain C and (resseq 5:395 )CC

NCS oper:
IDCodeMatrixVector
1given(-0.489878, 0.871584, 0.019004), (-0.871728, -0.489989, 0.001343), (0.010482, -0.015909, 0.999819)99.778297, 24.567699, -0.413134
2given(0.497723, -0.867267, -0.010969), (-0.867332, -0.497717, -0.003457), (-0.002461, 0.011234, -0.999934)71.570503, 24.417, -0.001805

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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-GDU / GALACTOSE-URIDINE-5'-DIPHOSPHATE / UDP-D-GALACTOPYRANOSE


Mass: 566.302 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C15H24N2O17P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.92 Å3/Da / Density % sol: 57.82 %
Crystal growTemperature: 277 K / Method: hanging drop vapor diffusion / pH: 5.5
Details: 0.1M Bis-Tris pH 5.5, 17.5% PEG 3350, 0-0.2M Ammonium acetate, 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: 2.6→48.572 Å / Num. all: 48236 / Num. obs: 48236 / % possible obs: 98.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 64.85 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Χ2: 1.009 / Net I/σ(I): 11.27
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.6-2.670.821.7412179350197.8
2.67-2.740.6892.1212461346698.5
2.74-2.820.5032.7212281339599.1
2.82-2.910.3963.4111795325398.9
2.91-30.3084.2911514317599
3-3.110.2395.4311233310298.9
3.11-3.220.1816.9410594296498.9
3.22-3.360.1358.8610204285199.3
3.36-3.510.09911.789164270697.5
3.51-3.680.08213.868896261798.2
3.68-3.880.07115.738353245597.6
3.88-4.110.05918.188002234897.8
4.11-4.390.04920.897653221199
4.39-4.750.04722.137334210899.6
4.75-5.20.04622.436729191899
5.2-5.810.04521.886088171999.1
5.81-6.710.04122.415499155299.2
6.71-8.220.03324.864624130199.1
8.22-11.630.0327.313571101699.2
11.630.02827.37195557898

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4rpg


Resolution: 2.6→48.572 Å / SU ML: 0.45 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.246 2410 5 %RANDOM
Rwork0.2076 ---
all0.2095 48236 --
obs0.2095 48212 98.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.1 Å2 / Biso mean: 65.3119 Å2 / Biso min: 30.55 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9573 0 267 130 9970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210152
X-RAY DIFFRACTIONf_angle_d0.61213846
X-RAY DIFFRACTIONf_chiral_restr0.0261440
X-RAY DIFFRACTIONf_plane_restr0.0031784
X-RAY DIFFRACTIONf_dihedral_angle_d17.9233912
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B3177X-RAY DIFFRACTIONPOSITIONAL0.465
12A3177X-RAY DIFFRACTIONPOSITIONAL0.465
13C3177X-RAY DIFFRACTIONPOSITIONAL0.554
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.66040.42451570.34852988314598
2.6604-2.7270.36691590.31243025318498
2.727-2.80070.38761600.29483042320299
2.8007-2.88310.31611620.27573069323199
2.8831-2.97610.30491590.26183032319199
2.9761-3.08250.34051610.26693046320799
3.0825-3.20590.32971620.26013079324199
3.2059-3.35180.27591590.24323029318899
3.3518-3.52840.2941590.2263018317798
3.5284-3.74940.2611600.22783047320799
3.7494-4.03880.26631580.20743009316797
4.0388-4.4450.21281610.17783064322599
4.445-5.08760.18031630.16173087325099
5.0876-6.40750.23771630.19243103326699
6.4075-48.58040.16931670.16043164333199

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