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- PDB-3ukq: Crystal structure of R327K UDP-galactopyranose mutase from Asperg... -

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Basic information

Entry
Database: PDB / ID: 3ukq
TitleCrystal structure of R327K UDP-galactopyranose mutase from Aspergillus fumigatus in complex with UDPgalp
ComponentsUDP-galactopyranose mutase
KeywordsISOMERASE / FLAVOENZYME / FAD
Function / homology
Function and homology information


UDP-galactopyranose mutase / UDP-galactopyranose mutase activity / cell wall organization / 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
FLAVIN-ADENINE DINUCLEOTIDE / GALACTOSE-URIDINE-5'-DIPHOSPHATE / UDP-galactopyranose mutase
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsVan Straaten, K.E. / Sanders, D.A.R.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Insight into the Unique Substrate Binding Mechanism and Flavin Redox State of UDP-galactopyranose Mutase from Aspergillus fumigatus.
Authors: van Straaten, K.E. / Routier, F.H. / Sanders, D.A.
History
DepositionNov 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2012Group: Database references
Revision 1.2Jul 18, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 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
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
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)233,06112
Polymers227,6534
Non-polymers5,4078
Water1,24369
1
A: UDP-galactopyranose mutase
C: UDP-galactopyranose mutase
hetero molecules

B: UDP-galactopyranose mutase
D: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,06112
Polymers227,6534
Non-polymers5,4078
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area18430 Å2
ΔGint-100 kcal/mol
Surface area76860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.540, 135.480, 176.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and (resseq 2:511 ) and (not element H) and (not element D)
211chain 'B' and (resseq 2:511 ) and (not element H) and (not element D)
311chain 'C' and (resseq 2:511 ) and (not element H) and (not element D)
411chain 'D' and (resseq 2:511 ) and (not element H) and (not element D)

NCS oper:
IDCodeMatrixVector
1given(0.999912, 0.011208, 0.007157), (-0.010576, 0.99649, -0.083044), (-0.008062, 0.082961, 0.99652)-1.60081, -62.312698, -26.935699
2given(-0.934719, 0.060723, -0.350162), (-0.036387, -0.996469, -0.075669), (-0.353521, -0.057988, 0.933628)134.656998, 111.362, 28.551901
3given(-0.940522, 0.036682, -0.337747), (-0.025687, -0.998986, -0.036968), (-0.338761, -0.026093, 0.940511)139.143005, 178.255005, 10.4004

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Components

#1: Protein
UDP-galactopyranose mutase


Mass: 56913.293 Da / Num. of mol.: 4 / Mutation: R327K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Strain: CBS 144-89 / Gene: glf, glfA / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) GOLD / References: UniProt: Q4W1X2, UDP-galactopyranose mutase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / 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.: 4
Source method: isolated from a genetically manipulated source
Formula: C15H24N2O17P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 3.39 Å3/Da / Density % sol: 63.77 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 8.5
Details: 0.1M Bis-Tris-Propane pH 7.5-8.5, 0.1-0.2M sodium citrate, 15-20% PEG 3350, microbatch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97934 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 3, 2011 / Details: collimating mirror
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.86→44.4 Å / Num. obs: 71880 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.198 / Rsym value: 0.198 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.86-2.930.021.15198.8
2.93-3.010.021.31198.3
3.01-3.10.022.1198.4
3.1-3.20.022.5199.6
3.2-3.30.023.43199.7
3.3-3.420.024.15199.7
3.42-3.550.025.33199.9
3.55-3.690.026.94199.8
3.69-3.860.028.17199.6
3.86-4.040.029.19199.8
4.04-4.260.0211199.8
4.26-4.520.0213.55199.9
4.52-4.830.0213.99199.7
4.83-5.220.0214.23199.9
5.22-5.720.0213.65199.9
5.72-6.40.0213.361100
6.4-7.380.0215.21100
7.38-9.040.0221.191100
9.04-12.790.0227.72199.9
12.79-44.40.0225.67197.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
MxDCdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: reduced AfUGM:UDPgalp structure

Highest resolution: 3.15 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.4 / Isotropic thermal model: Isotropic / σ(F): 1.99 / Phase error: 26.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2482 2705 5 %
Rwork0.2116 --
obs0.2135 54080 99.66 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.493 Å2 / ksol: 0.355 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--24.5503 Å20 Å2-0 Å2
2--38.359 Å2-0 Å2
3----14.0976 Å2
Refinement stepCycle: LAST / Highest resolution: 3.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16008 0 356 69 16433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416788
X-RAY DIFFRACTIONf_angle_d0.73822880
X-RAY DIFFRACTIONf_dihedral_angle_d19.5836464
X-RAY DIFFRACTIONf_chiral_restr0.0512480
X-RAY DIFFRACTIONf_plane_restr0.0032916
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A4002X-RAY DIFFRACTIONPOSITIONAL
12B4002X-RAY DIFFRACTIONPOSITIONAL0.239
13C4002X-RAY DIFFRACTIONPOSITIONAL0.283
14D4002X-RAY DIFFRACTIONPOSITIONAL0.287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1501-3.26270.30742670.28545070X-RAY DIFFRACTION100
3.2627-3.39330.32192650.26545056X-RAY DIFFRACTION100
3.3933-3.54760.31572670.24075064X-RAY DIFFRACTION100
3.5476-3.73460.25042670.22385094X-RAY DIFFRACTION100
3.7346-3.96850.25482690.20365095X-RAY DIFFRACTION100
3.9685-4.27480.24162690.19475108X-RAY DIFFRACTION100
4.2748-4.70460.21722700.18445120X-RAY DIFFRACTION100
4.7046-5.38460.20652720.18145166X-RAY DIFFRACTION100
5.3846-6.78120.24992750.20715221X-RAY DIFFRACTION100
6.7812-48.69860.22852840.20695381X-RAY DIFFRACTION100

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