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- PDB-3ukh: Crystal structure of udp-galactopyranose mutase from Aspergillus ... -

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Basic information

Entry
Database: PDB / ID: 3ukh
TitleCrystal structure of udp-galactopyranose mutase from Aspergillus fumigatus in complex with UDPGALP (non-reduced)
ComponentsUDP-galactopyranose mutase
KeywordsISOMERASE / FLAVOENZYME / FAD / FADH2 ISOMERASE
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
FLAVIN-ADENINE DINUCLEOTIDE / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / GALACTOSE-URIDINE-5'-DIPHOSPHATE / UDP-galactopyranose mutase
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.3Feb 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
Revision 1.4Apr 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
E: UDP-galactopyranose mutase
F: UDP-galactopyranose mutase
G: UDP-galactopyranose mutase
H: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)476,02326
Polymers465,1338
Non-polymers10,89018
Water23,0231278
1
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)238,04714
Polymers232,5664
Non-polymers5,48010
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18510 Å2
ΔGint-135 kcal/mol
Surface area80360 Å2
MethodPISA
2
E: UDP-galactopyranose mutase
F: UDP-galactopyranose mutase
G: UDP-galactopyranose mutase
H: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,97612
Polymers232,5664
Non-polymers5,4098
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18190 Å2
ΔGint-114 kcal/mol
Surface area81260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.967, 129.262, 173.885
Angle α, β, γ (deg.)89.87, 84.64, 81.21
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 2:200 or resseq 208:312 or resseq...
211chain B and (resseq 2:200 or resseq 208:312 or resseq...
311chain C and (resseq 2:200 or resseq 208:312 or resseq...
411chain D and (resseq 2:200 or resseq 208:312 or resseq...
511chain E and (resseq 2:200 or resseq 208:312 or resseq...
611chain F and (resseq 2:200 or resseq 208:312 or resseq...
711chain G and (resseq 2:200 or resseq 208:312 or resseq...
811chain H and (resseq 2:200 or resseq 208:312 or resseq...

NCS oper:
IDCodeMatrixVector
1given(-0.963105, 0.266564, 0.037052), (0.261826, 0.896206, 0.358137), (0.06226, 0.354624, -0.932934)34.960701, -10.8775, 31.8948
2given(-0.979848, 0.018865, 0.198849), (-0.096032, -0.917415, -0.38617), (0.175142, -0.397484, 0.900739)39.011101, 64.271896, 9.65289
3given(0.933591, -0.286165, -0.215678), (-0.286846, -0.957543, 0.028834), (-0.214772, 0.034947, -0.976039)14.108, 60.504002, 47.832401
4given(0.943363, -0.298136, -0.145536), (-0.225811, -0.898395, 0.37669), (-0.243054, -0.322492, -0.914835)30.0131, 17.542999, -50.163799
5given(-0.983361, 0.034864, 0.178287), (-0.041922, -0.998473, -0.035976), (0.176761, -0.042851, 0.983321)7.25025, -5.70841, 86.355698
6given(-0.96133, 0.273931, -0.028382), (0.274013, 0.961725, 0.001046), (0.027582, -0.006772, -0.999597)2.33649, 64.447304, -38.361099
7given(0.999906, -0.000599, 0.013697), (0.005616, 0.929269, -0.36936), (-0.012508, 0.369402, 0.929185)50.2952, 33.2202, 90.067398

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
UDP-galactopyranose mutase


Mass: 58141.594 Da / Num. of mol.: 8 / Fragment: udpgalactopyranose mutase
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

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Non-polymers , 5 types, 1296 molecules

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


Mass: 785.550 Da / Num. of mol.: 6 / 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.: 8
Source method: isolated from a genetically manipulated source
Formula: C15H24N2O17P2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1278 / 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: 3.42 Å3/Da / Density % sol: 64.05 %
Crystal growTemperature: 295 K / pH: 8.5
Details: 0.1M Bis-Tris-Propane pH 8.5, 0.2M NaNO2, 20% PEG 3350, microbatch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 5, 2009 / Details: DOUBLE CRYSTAL MONOCHROMATOR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→35.548 Å / Num. obs: 266596 / % possible obs: 97.3 % / Observed criterion σ(I): 1 / Redundancy: 3.94 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 8.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.85 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 2.6 / % possible all: 88.4

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
d*TREK9.9.8.0Ldata reduction
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PARTIALLY REFINED MODEL FROM LMUGM

Resolution: 2.3→35.548 Å / Occupancy max: 1 / Occupancy min: 0.35 / SU ML: 0.94 / Isotropic thermal model: Isotropic / σ(F): 1.96 / Phase error: 30.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2641 13327 5 %
Rwork0.2218 --
obs0.2239 266467 97.28 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.86 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-17.8455 Å2-13.1287 Å2-2.2817 Å2
2---4.8225 Å20.1451 Å2
3----6.0308 Å2
Refinement stepCycle: LAST / Resolution: 2.3→35.548 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31926 0 714 1278 33918
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00434500
X-RAY DIFFRACTIONf_angle_d0.76647053
X-RAY DIFFRACTIONf_dihedral_angle_d17.75413174
X-RAY DIFFRACTIONf_chiral_restr0.0535090
X-RAY DIFFRACTIONf_plane_restr0.0056007
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A4039X-RAY DIFFRACTIONPOSITIONAL
12B4039X-RAY DIFFRACTIONPOSITIONAL0.477
13C3877X-RAY DIFFRACTIONPOSITIONAL0.489
14D3857X-RAY DIFFRACTIONPOSITIONAL0.3
15E3968X-RAY DIFFRACTIONPOSITIONAL0.398
16F3862X-RAY DIFFRACTIONPOSITIONAL0.316
17G3856X-RAY DIFFRACTIONPOSITIONAL0.301
18H3839X-RAY DIFFRACTIONPOSITIONAL0.463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.38220.435412180.389323049X-RAY DIFFRACTION88
2.3822-2.47760.403713530.347825378X-RAY DIFFRACTION98
2.4776-2.59030.36213600.311125425X-RAY DIFFRACTION98
2.5903-2.72680.330913000.279425561X-RAY DIFFRACTION98
2.7268-2.89760.325814420.263325544X-RAY DIFFRACTION98
2.8976-3.12120.296913390.246625620X-RAY DIFFRACTION98
3.1212-3.4350.285312920.234725742X-RAY DIFFRACTION99
3.435-3.93150.25713360.220525699X-RAY DIFFRACTION99
3.9315-4.95120.215313110.172525744X-RAY DIFFRACTION99
4.9512-35.55240.211413760.185925378X-RAY DIFFRACTION98

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