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- PDB-3ukp: Crystal structure of R327A UDP-galactopyranose mutase from Asperg... -

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Basic information

Entry
Database: PDB / ID: 3ukp
TitleCrystal structure of R327A 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: 3.1 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
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)463,61822
Polymers453,9368
Non-polymers9,68214
Water00
1
A: UDP-galactopyranose mutase
C: UDP-galactopyranose mutase
E: UDP-galactopyranose mutase
G: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,80911
Polymers226,9684
Non-polymers4,8417
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16560 Å2
ΔGint-101 kcal/mol
Surface area79580 Å2
MethodPISA
2
B: UDP-galactopyranose mutase
D: UDP-galactopyranose mutase
F: UDP-galactopyranose mutase
H: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,80911
Polymers226,9684
Non-polymers4,8417
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16840 Å2
ΔGint-101 kcal/mol
Surface area79290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.600, 175.710, 135.347
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 2:357 or resseq 360: 511 ) and (not element H) and (not element D)
211chain B and (resseq 2:357 or resseq 360: 511 ) and (not element H) and (not element D)
311chain C and (resseq 2:357 or resseq 360: 511 ) and (not element H) and (not element D)
411chain D and (resseq 2:357 or resseq 360: 511 ) and (not element H) and (not element D)
112chain E and (resseq 2:357 or resseq 360: 511 ) and (not element H) and (not element D)
212chain F and (resseq 2:357 or resseq 360: 511 ) and (not element H) and (not element D)
113chain G and (resseq 2:357 or resseq 360: 511 ) and (not element H) and (not element D)
213chain H and (resseq 2:357 or resseq 360: 511 ) and (not element H) and (not element D)

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(0.999891, 0.005584, -0.013692), (-0.007165, 0.992957, -0.118259), (0.012935, 0.118344, 0.992888)1.3372, 1.89876, -78.0662
2given(-0.999166, -0.002086, -0.040785), (0.007322, -0.991661, -0.128663), (-0.040176, -0.128855, 0.990849)68.323898, 159.473007, 11.9035
3given(-0.999705, 0.005893, -0.023577), (-0.005494, -0.999841, -0.016971), (-0.023673, -0.016837, 0.999578)67.9328, 169.248001, -65.153603
4given(0.999789, 0.011689, -0.016909), (-0.012412, 0.998987, -0.043248), (0.016387, 0.043449, 0.998921)1.47464, -9.98436, -73.400703
5given(0.99955, -0.020648, -0.021744), (0.019253, 0.997858, -0.062516), (0.022988, 0.062069, 0.997807)5.17333, -8.42968, -73.988998

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Components

#1: Protein
UDP-galactopyranose mutase


Mass: 56742.035 Da / Num. of mol.: 8 / Mutation: R327A
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.: 8 / 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.: 6
Source method: isolated from a genetically manipulated source
Formula: C15H24N2O17P2

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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 / pH: 8.5
Details: 0.1M Bis-Tris- propane pH 7.5-8.5, 0.1-0.2M sodium citrate, 15-20% PEG 3350, micro batch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9798 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 10, 2011 / Details: collimating mirror
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.479
ReflectionResolution: 3.1→34.77 Å / Num. obs: 105656 / % possible obs: 96.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.38 % / Rmerge(I) obs: 0.238 / Rsym value: 0.238 / Net I/σ(I): 3.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.1-3.213.430.631.7198.1
3.21-3.343.420.5662197.9
3.34-3.493.410.4932.3197.5
3.49-3.673.380.4272.7197.4
3.67-3.93.350.3533.1197.1
3.9-4.213.320.3073.5196.6
4.21-4.633.310.2514.1195.9
4.63-5.33.350.2294.4195.4
5.3-6.663.430.2244.5195.2
6.66-34.773.360.1147191.8

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
d*TREK9.9.8.0Ldata reduction
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
MxDCdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: reduced AfUGM:UDPgalp complex

Resolution: 3.1→34.77 Å / Occupancy max: 1 / Occupancy min: 0.69 / Isotropic thermal model: Isotropic / σ(F): 0 / Phase error: 22.19 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.26 5435 5.15 %
Rwork0.202 --
obs0.206 105627 96.3 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.38 Å2 / ksol: 0.32 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.0828 Å2-0 Å23.9557 Å2
2---19.7586 Å20 Å2
3---25.8414 Å2
Refinement stepCycle: LAST / Resolution: 3.1→34.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31920 0 640 0 32560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00533404
X-RAY DIFFRACTIONf_angle_d1.14845524
X-RAY DIFFRACTIONf_dihedral_angle_d20.85912478
X-RAY DIFFRACTIONf_chiral_restr0.0814926
X-RAY DIFFRACTIONf_plane_restr0.0055822
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3975X-RAY DIFFRACTIONPOSITIONAL
12B3975X-RAY DIFFRACTIONPOSITIONAL0.15
13C3975X-RAY DIFFRACTIONPOSITIONAL0.131
14D3975X-RAY DIFFRACTIONPOSITIONAL0.116
21E3975X-RAY DIFFRACTIONPOSITIONAL
22F3975X-RAY DIFFRACTIONPOSITIONAL0.167
31G3975X-RAY DIFFRACTIONPOSITIONAL
32H3975X-RAY DIFFRACTIONPOSITIONAL0.174
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1001-3.15350.32072730.26165092X-RAY DIFFRACTION93
3.1535-3.21080.33023190.25635075X-RAY DIFFRACTION92
3.2108-3.27240.31732960.24335011X-RAY DIFFRACTION93
3.2724-3.33920.28812520.23265130X-RAY DIFFRACTION93
3.3392-3.41170.28162580.23855134X-RAY DIFFRACTION93
3.4117-3.49090.27552400.22635010X-RAY DIFFRACTION93
3.4909-3.57810.28162920.22125049X-RAY DIFFRACTION92
3.5781-3.67470.26492650.21955053X-RAY DIFFRACTION92
3.6747-3.78260.26692700.20915043X-RAY DIFFRACTION92
3.7826-3.90450.26882410.20425098X-RAY DIFFRACTION92
3.9045-4.04380.26452530.20065011X-RAY DIFFRACTION92
4.0438-4.20530.25412790.18635000X-RAY DIFFRACTION91
4.2053-4.39610.25542720.17764980X-RAY DIFFRACTION91
4.3961-4.62720.21852690.16934996X-RAY DIFFRACTION91
4.6272-4.9160.22132660.17354955X-RAY DIFFRACTION90
4.916-5.29380.22552660.18044953X-RAY DIFFRACTION91
5.2938-5.82320.27082280.19125029X-RAY DIFFRACTION91
5.8232-6.65840.29872840.21244945X-RAY DIFFRACTION90
6.6584-8.36060.25142620.19774925X-RAY DIFFRACTION89
8.3606-30.67850.22032480.18134768X-RAY DIFFRACTION85

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