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- PDB-5eqd: Structure of oxidized UDP-galactopyranose mutase from Mycobacteri... -

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Basic information

Entry
Database: PDB / ID: 5eqd
TitleStructure of oxidized UDP-galactopyranose mutase from Mycobacterium smegmatis in complex with UDP in opened and closed form
ComponentsUDP-galactopyranose mutase
KeywordsISOMERASE / galactofuranose
Function / homology
Function and homology information


UDP-galactopyranose mutase / UDP-galactopyranose mutase activity / flavin adenine dinucleotide binding / metal ion 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 / NITRATE ION / URIDINE-5'-DIPHOSPHATE / UDP-galactopyranose mutase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.83 Å
AuthorsWangkanont, K. / Kiessling, L.L. / Forest, K.T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI063596 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM100346 United States
CitationJournal: to be published
Title: Structural dynamics of UDP-galactopyranose mutase from Mycobacterium smegmatis
Authors: Wangkanont, K. / Kiessling, L.L. / Forest, K.T.
History
DepositionNov 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,73718
Polymers91,7522
Non-polymers2,98616
Water13,331740
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7550 Å2
ΔGint-69 kcal/mol
Surface area32090 Å2
2
A: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1028
Polymers45,8761
Non-polymers1,2267
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,63610
Polymers45,8761
Non-polymers1,7609
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.188, 132.184, 135.654
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-504-

SO4

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein UDP-galactopyranose mutase / UDP-galactopyranose mutase Glf


Mass: 45875.906 Da / Num. of mol.: 2 / Fragment: residues 13-412
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: glf, MSMEG_6404, MSMEI_6236 / Plasmid: pMAL c5x
Details (production host): malE ORF in pMAL c5x was removed and replaced with the ORF for UDP-galactopyranose mutase
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0R629, UDP-galactopyranose mutase

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Non-polymers , 5 types, 756 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: NO3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 740 / 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: 3.03 Å3/Da / Density % sol: 59.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris-HCl, 100 mM sodium nitrate, 1.8 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.978542 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 12, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978542 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 96510 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 24.63 Å2 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.035 / Rrim(I) all: 0.095 / Χ2: 1.125 / Net I/av σ(I): 23.269 / Net I/σ(I): 8.7 / Num. measured all: 699321
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.83-1.926.80.69495680.8440.2860.7520.724100
1.92-1.996.90.47295740.9170.1930.510.791100
1.99-2.0870.32895600.9590.1330.3540.87100
2.08-2.197.10.23595850.9760.0940.2540.966100
2.19-2.337.30.18796030.9830.0740.2011.126100
2.33-2.517.50.14795840.9890.0580.1581.186100
2.51-2.767.50.11196690.9930.0430.1191.16100
2.76-3.167.60.09396530.9950.0360.11.511100
3.16-3.997.50.06897080.9970.0270.0731.587100
3.99-507.30.054100060.9970.0210.0581.20399.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.5.6phasing
PHENIX(phenix.refine: 1.9_1690)refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I8T

1i8t


Resolution: 1.83→45.8 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1958 4651 5.02 %
Rwork0.1682 87981 -
obs0.1696 92632 94.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.22 Å2 / Biso mean: 29.4299 Å2 / Biso min: 14.36 Å2
Refinement stepCycle: final / Resolution: 1.83→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6365 0 189 740 7294
Biso mean--33.87 36.31 -
Num. residues----783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076836
X-RAY DIFFRACTIONf_angle_d1.0599322
X-RAY DIFFRACTIONf_chiral_restr0.045949
X-RAY DIFFRACTIONf_plane_restr0.0051220
X-RAY DIFFRACTIONf_dihedral_angle_d14.432438
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8298-1.89520.26463460.23126636698272
1.8952-1.97110.26184550.20858346880190
1.9711-2.06080.22864560.19038633908993
2.0608-2.16940.21054590.17718815927495
2.1694-2.30530.20794800.17228955943597
2.3053-2.48330.20614710.17739115958698
2.4833-2.73320.21794840.18549154963899
2.7332-3.12860.22914920.18949307979999
3.1286-3.94140.18154950.157293769871100
3.9414-45.81430.15355130.1397964410157100

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