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- PDB-3mj4: Crystal structure of UDP-galactopyranose mutase in complex with p... -

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Basic information

Entry
Database: PDB / ID: 3mj4
TitleCrystal structure of UDP-galactopyranose mutase in complex with phosphonate analog of UDP-galactopyranose
ComponentsUDP-galactopyranose mutase
KeywordsISOMERASE / UDP-galactopyranose mutase / phosphonate analog / inhibitor / binding mode
Function / homology
Function and homology information


UDP-galactopyranose mutase activity / flavin adenine dinucleotide binding / 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 / Chem-URM / Xylitol / UDP-galactopyranose mutase
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsKarunan Partha, S. / Sadeghi-Khomami, A. / Slowski, K. / Kotake, T. / Thomas, N.R. / Jakeman, D.L. / Sanders, D.A.R.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Chemoenzymatic Synthesis, Inhibition Studies, and X-ray Crystallographic Analysis of the Phosphono Analog of UDP-Galp as an Inhibitor and Mechanistic Probe for UDP-Galactopyranose Mutase.
Authors: Partha, S.K. / Sadeghi-Khomami, A. / Slowski, K. / Kotake, T. / Thomas, N.R. / Jakeman, D.L. / Sanders, D.A.
History
DepositionApr 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-galactopyranose mutase
B: UDP-galactopyranose mutase
C: UDP-galactopyranose mutase
D: UDP-galactopyranose mutase
E: UDP-galactopyranose mutase
F: UDP-galactopyranose mutase
G: UDP-galactopyranose mutase
H: UDP-galactopyranose mutase
I: UDP-galactopyranose mutase
J: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)472,08257
Polymers457,41810
Non-polymers14,66447
Water11,043613
1
A: UDP-galactopyranose mutase
I: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,66014
Polymers91,4842
Non-polymers3,17612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint-32 kcal/mol
Surface area29870 Å2
MethodPISA
2
B: UDP-galactopyranose mutase
H: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1399
Polymers91,4842
Non-polymers2,6567
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7490 Å2
ΔGint-36 kcal/mol
Surface area30260 Å2
MethodPISA
3
C: UDP-galactopyranose mutase
F: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,38411
Polymers91,4842
Non-polymers2,9009
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7540 Å2
ΔGint-35 kcal/mol
Surface area29760 Å2
MethodPISA
4
D: UDP-galactopyranose mutase
J: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,39210
Polymers91,4842
Non-polymers2,9088
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-29 kcal/mol
Surface area29880 Å2
MethodPISA
5
E: UDP-galactopyranose mutase
G: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,50813
Polymers91,4842
Non-polymers3,02411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7570 Å2
ΔGint-33 kcal/mol
Surface area29640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.149, 175.715, 223.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 12 molecules ABCDEFGHIJ

#1: Protein
UDP-galactopyranose mutase /


Mass: 45741.824 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: R1 / Gene: DR_A0367, DR_AO367 / Plasmid: PEHISTEV / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner / References: UniProt: Q9RYF1, UDP-galactopyranose mutase
#6: Sugar ChemComp-XYL / Xylitol / D-Xylitol / Xylitol


Type: D-saccharide / Mass: 152.146 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H12O5

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Non-polymers , 5 types, 658 molecules

#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-URM / (((2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl)methyl)phosphonic (((2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl phosphoric) anhydride / Uridine diphospho methylene galactopyranose


Mass: 564.329 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H26N2O16P2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 613 / 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: 2.88 Å3/Da / Density % sol: 57.35 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 6.5
Details: 0.1 M HEPES PH 6.5, 0.2 M LICL, 28% PEG 6000, Microbatch, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.6→102.06 Å / Num. obs: 162540 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.166 / Net I/σ(I): 5.8
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.617 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameClassification
MOLREPphasing
PHENIXrefinement
MxDCdata collection
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HDQ

3hdq


Resolution: 2.65→44.542 Å / SU ML: 0.47 / σ(F): 0 / Phase error: 28.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2622 7710 5.02 %
Rwork0.207 --
obs0.2098 153502 99.9 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.251 Å2 / ksol: 0.408 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.8076 Å2-0 Å20 Å2
2---8.9448 Å2-0 Å2
3---9.7524 Å2
Refinement stepCycle: LAST / Resolution: 2.65→44.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29674 0 953 613 31240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00831530
X-RAY DIFFRACTIONf_angle_d1.2342966
X-RAY DIFFRACTIONf_dihedral_angle_d16.6911596
X-RAY DIFFRACTIONf_chiral_restr0.0784464
X-RAY DIFFRACTIONf_plane_restr0.0055509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.74470.45387610.381614445X-RAY DIFFRACTION100
2.7447-2.85460.41167920.345614400X-RAY DIFFRACTION100
2.8546-2.98450.35437960.276914458X-RAY DIFFRACTION100
2.9845-3.14180.3437390.263914491X-RAY DIFFRACTION100
3.1418-3.33860.30457640.224114502X-RAY DIFFRACTION100
3.3386-3.59620.27127620.205614528X-RAY DIFFRACTION100
3.5962-3.95790.27097300.213714607X-RAY DIFFRACTION100
3.9579-4.53020.20087860.148914615X-RAY DIFFRACTION100
4.5302-5.70570.19948020.152214691X-RAY DIFFRACTION100
5.7057-44.54870.23237780.201615055X-RAY DIFFRACTION99

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