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

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Basic information

Entry
Database: PDB / ID: 4rpg
TitleCrystal structure of Micobacterium tuberculosis UDP-Galactopyranose mutase in complex with substrate UDP-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
FLAVIN-ADENINE DINUCLEOTIDE / GALACTOSE-URIDINE-5'-DIPHOSPHATE / URIDINE-5'-DIPHOSPHATE / UDP-galactopyranose mutase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4001 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 1.4Feb 28, 2024Group: 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 / 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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)141,5169
Polymers137,7853
Non-polymers3,7316
Water7,116395
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
Buried area7010 Å2
ΔGint-38 kcal/mol
Surface area30060 Å2
MethodPISA
2
A: UDP-galactopyranose mutase
C: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,2366
Polymers91,8572
Non-polymers2,3794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-35 kcal/mol
Surface area30360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.420, 99.470, 100.160
Angle α, β, γ (deg.)90.00, 110.81, 90.00
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(-0.497804, 0.867212, 0.01163), (-0.867287, -0.49779, -0.004243), (0.00211, -0.012199, 0.999923)100.217003, 25.312599, -0.155435
2given(0.494288, -0.869298, 0.000137), (-0.869298, -0.494287, 0.00053), (-0.000393, -0.000381, -1)72.186203, 25.307899, 0.086628

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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 / Fragment: UDP-Galactopyranose Mutase / 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.: 1
Source method: isolated from a genetically manipulated source
Formula: C15H24N2O17P2
#4: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.91 Å3/Da / Density % sol: 57.78 %
Crystal growTemperature: 277 K / Method: hanging drop vapor diffusion / pH: 5.5
Details: 0.1M Bis-Tris pH 5.5, 20% PEG 3350, 10mM Phenol, 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: Jan 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.4→47.3 Å / Num. all: 61216 / Num. obs: 61216 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 48.2 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 9.68
Reflection shellResolution: 2.4→2.46 Å / % possible obs: 98.8 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.764 / Mean I/σ(I) obs: 1.6 / Num. measured all: 4478 / Num. measured obs: 4478 / % possible all: 98.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
MxDCdata collection
AutoProcessdata reduction
AutoProcessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VOJ

1voj


Resolution: 2.4001→47.27 Å / FOM work R set: 0.7805 / SU ML: 0.37 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2374 3061 5 %RANDOM
Rwork0.1946 ---
all0.1967 61216 --
obs0.1967 61181 98.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.63 Å2 / Biso mean: 51.61 Å2 / Biso min: 27.54 Å2
Refinement stepCycle: LAST / Resolution: 2.4001→47.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9597 0 245 395 10237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310146
X-RAY DIFFRACTIONf_angle_d0.77513832
X-RAY DIFFRACTIONf_chiral_restr0.0291437
X-RAY DIFFRACTIONf_plane_restr0.0041783
X-RAY DIFFRACTIONf_dihedral_angle_d15.9813892
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B3196X-RAY DIFFRACTIONPOSITIONAL0.327
12A3196X-RAY DIFFRACTIONPOSITIONAL0.327
13C3180X-RAY DIFFRACTIONPOSITIONAL0.328
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4001-2.44150.38881520.30942894304699
2.4415-2.48590.40661520.31772879303199
2.4859-2.53370.3751520.29232881303399
2.5337-2.58540.3321520.28112874302699
2.5854-2.64160.34211530.27422901305499
2.6416-2.7030.31251520.26722901305399
2.703-2.77060.32261540.25282909306399
2.7706-2.84550.31881510.26112886303799
2.8455-2.92920.36071530.24352906305998
2.9292-3.02380.27581520.24172886303899
3.0238-3.13180.26191520.2312886303898
3.1318-3.25720.27411510.23172859301099
3.2572-3.40540.28311520.20782885303798
3.4054-3.58490.23991530.19912924307799
3.5849-3.80940.25271540.1912919307399
3.8094-4.10340.17561520.16782887303999
4.1034-4.5160.18291550.14262938309399
4.516-5.16880.16921530.14182911306499
5.1688-6.50940.19781560.1672964312099
6.5094-47.27870.17921600.152130303190100

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