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- PDB-3ute: Crystal structure of Aspergillus fumigatus UDP galactopyranose mu... -

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Basic information

Entry
Database: PDB / ID: 3ute
TitleCrystal structure of Aspergillus fumigatus UDP galactopyranose mutase sulfate complex
ComponentsUDP-galactopyranose mutase
KeywordsISOMERASE / Nucleotide binding / Mutase / Flavin adenine dinucleotide binding
Function / homology
Function and homology information


UDP-galactopyranose mutase / UDP-galactopyranose mutase activity / nucleotide binding
Similarity search - Function
NAD(P)-binding Rossmann-like domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / UDP-galactopyranose mutase
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsDhatwalia, R. / Singh, H. / Tanner, J.J.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal Structures and Small-angle X-ray Scattering Analysis of UDP-galactopyranose Mutase from the Pathogenic Fungus Aspergillus fumigatus.
Authors: Dhatwalia, R. / Singh, H. / Oppenheimer, M. / Karr, D.B. / Nix, J.C. / Sobrado, P. / Tanner, J.J.
History
DepositionNov 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2012Group: Database references
Revision 1.2Apr 4, 2012Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,44027
Polymers228,5144
Non-polymers4,92623
Water9,296516
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17480 Å2
ΔGint-319 kcal/mol
Surface area75390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)217.841, 217.841, 319.693
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-516-

ACT

21B-516-

ACT

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
UDP-galactopyranose mutase /


Mass: 57128.484 Da / Num. of mol.: 4 / Mutation: K344A, K345A, A429T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: glf, glfA / Plasmid: pVP56K / Production host: Escherichia coli (E. coli) / References: UniProt: Q4W1X2, UDP-galactopyranose mutase

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Non-polymers , 5 types, 539 molecules

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


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 516 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHOR STATES THAT A429T IS AN UNINTENDED MUTATION ON THE SURFACE OF THE PROTEIN.

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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: 4.79 Å3/Da / Density % sol: 74.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 1.5M ammonium sulfate, 0.1M sodium acetate, 5mM L-cysteine, 0.5mM THP , pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 6, 2011 / Details: Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 167455 / % possible obs: 90.5 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.086 / Χ2: 1.017 / Net I/σ(I): 8.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.35-2.435.40.568166670.59191.1
2.43-2.535.40.427166640.593191.3
2.53-2.655.40.325166950.615191.3
2.65-2.795.40.24167850.644191.5
2.79-2.965.40.163167700.674191.3
2.96-3.195.40.111167990.811191.3
3.19-3.515.40.08167601.155190.7
3.51-4.025.40.069166941.884190
4.02-5.065.30.054166592.057189
5.06-505.40.034169621.166187.3

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.6.2_432refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.35→49.421 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8482 / SU ML: 0.33 / σ(F): 0 / Phase error: 21.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2183 8395 5.02 %random
Rwork0.1881 ---
obs0.1896 167290 90.37 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.152 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso max: 144.47 Å2 / Biso mean: 34.984 Å2 / Biso min: 7.15 Å2
Baniso -1Baniso -2Baniso -3
1--5.6926 Å20 Å20 Å2
2---5.6926 Å2-0 Å2
3---11.3853 Å2
Refinement stepCycle: LAST / Resolution: 2.35→49.421 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15569 0 307 516 16392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716302
X-RAY DIFFRACTIONf_angle_d1.06422277
X-RAY DIFFRACTIONf_chiral_restr0.0682435
X-RAY DIFFRACTIONf_plane_restr0.0052870
X-RAY DIFFRACTIONf_dihedral_angle_d14.8375969
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 (%)
2.35-2.43070.29748050.2486156961650190
2.4307-2.5280.28018410.2198158361667791
2.528-2.6430.25158620.2079158381670091
2.643-2.78240.24198190.2015159751679491
2.7824-2.95670.24527990.2054159611676091
2.9567-3.18490.25198660.2146159411680791
3.1849-3.50540.2418670.2126158901675791
3.5054-4.01240.20927980.1791158831668190
4.0124-5.05440.16178610.1374158191668089
5.0544-49.43220.18958770.1769160561693387
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.67660.0016-0.2690.0759-0.0280.23610.02120.1918-0.049-0.0033-0.0226-0.0769-0.0211-0.02940.00390.05750.04730.02510.1926-0.0290.122471.423577.7283159.3665
20.2792-0.25860.01210.4220.01980.2317-0.0788-0.0460.04790.09870.04130.062-0.0023-0.0020.00820.08580.04770.02230.0724-0.02230.100624.4064103.2378211.9273
30.87210.1761-0.08520.15430.06940.324-0.03260.3585-0.1832-0.0010.06990.09040.1009-0.0236-0.0618-0.03880.0339-0.07170.2199-0.10250.055925.5668.0432149.5188
40.3171-0.25460.02970.68670.06590.1972-0.0934-0.0622-0.12560.22940.11710.1280.0234-0.0074-0.00670.17090.08630.05310.11840.07910.131241.926859.7539222.1384
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA3 - 507
2X-RAY DIFFRACTION2chain BB3 - 507
3X-RAY DIFFRACTION3chain CC3 - 506
4X-RAY DIFFRACTION4chain DD3 - 506

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