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

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Basic information

Entry
Database: PDB / ID: 4rpj
TitleCrystal structure of Micobacterium tuberculosis UDP-Galactopyranose mutase in complex with UDP
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 / URIDINE-5'-DIPHOSPHATE / UDP-galactopyranose mutase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 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 / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)141,3549
Polymers137,7853
Non-polymers3,5696
Water4,918273
1
B: UDP-galactopyranose mutase
hetero molecules

B: 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
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)94,2366
Polymers91,8572
Non-polymers2,3794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)176.483, 101.214, 102.056
Angle α, β, γ (deg.)90.00, 109.23, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and (resseq 4:396 )
211chain 'B' and (resseq 4:396 )
311chain 'C' and (resseq 4:396 )

NCS oper:
IDCodeMatrixVector
1given(-0.499864, -0.866104, 0.000216), (0.866104, -0.499864, -0.000641), (0.000663, -0.000134, 1)73.434097, -76.513298, -0.072461
2given(0.504179, 0.863598, 0.001135), (0.863582, -0.504177, 0.005714), (0.005507, -0.0019, -0.999983)14.7195, -25.5835, -0.207432

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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-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 3.12 Å3/Da / Density % sol: 60.62 %
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: Jan 30, 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: 2.5→45.532 Å / Num. all: 58458 / Num. obs: 58458 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.38 % / Biso Wilson estimate: 69.41 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.5-2.596.70.6872.21100
2.59-2.696.680.6112.51100
2.69-2.826.630.5013.11100
2.82-2.966.580.4213.71100
2.96-3.156.420.3284.7199.7
3.15-3.396.250.2446.2199.5
3.39-3.736.230.1688.8198.7
3.73-4.276.170.12811.4198.9
4.27-5.386.280.10815199.1
5.38-45.535.830.10616.2199.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREK9.9.9.7Ldata scaling
d*TREK9.9.9.7Ldata reduction
MOLREPphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
MxDCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MtUGM in complex with UDP-Galp (4RPG)

4rpg


Resolution: 2.5→45.532 Å / SU ML: 0.37 / Isotropic thermal model: Isotropic / σ(F): 1.39 / Phase error: 26.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2214 2934 5.02 %
Rwork0.1849 --
obs0.1868 58444 99.47 %
all-58458 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.31 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.532 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9615 0 234 273 10122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210137
X-RAY DIFFRACTIONf_angle_d0.60113815
X-RAY DIFFRACTIONf_dihedral_angle_d12.9313876
X-RAY DIFFRACTIONf_chiral_restr0.0231434
X-RAY DIFFRACTIONf_plane_restr0.0031783
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3205X-RAY DIFFRACTIONPOSITIONAL0.31
12B3205X-RAY DIFFRACTIONPOSITIONAL0.31
13C3205X-RAY DIFFRACTIONPOSITIONAL0.396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.5410.3961410.32072652X-RAY DIFFRACTION100
2.541-2.58480.34481510.29772628X-RAY DIFFRACTION100
2.5848-2.63180.33951400.28752643X-RAY DIFFRACTION100
2.6318-2.68240.32711520.26022642X-RAY DIFFRACTION100
2.6824-2.73720.28891270.2512649X-RAY DIFFRACTION100
2.7372-2.79670.3291450.25332607X-RAY DIFFRACTION100
2.7967-2.86170.29211490.2672649X-RAY DIFFRACTION100
2.8617-2.93330.37741220.28212680X-RAY DIFFRACTION100
2.9333-3.01260.33721450.27222611X-RAY DIFFRACTION100
3.0126-3.10120.31671300.2672655X-RAY DIFFRACTION100
3.1012-3.20130.29061500.24542654X-RAY DIFFRACTION100
3.2013-3.31560.26151290.23552622X-RAY DIFFRACTION100
3.3156-3.44840.29961460.23932634X-RAY DIFFRACTION99
3.4484-3.60520.25991380.21042628X-RAY DIFFRACTION99
3.6052-3.79520.26681360.19312629X-RAY DIFFRACTION99
3.7952-4.03290.21671410.17182607X-RAY DIFFRACTION99
4.0329-4.3440.181380.15792638X-RAY DIFFRACTION99
4.344-4.78080.15781370.13382638X-RAY DIFFRACTION99
4.7808-5.47150.17541370.14282650X-RAY DIFFRACTION99
5.4715-6.88970.19221400.16172688X-RAY DIFFRACTION99
6.8897-45.53930.1441400.13172706X-RAY DIFFRACTION99

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