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- PDB-3ukl: Crystal structure of UDP-galactopyranose mutase from Aspergillus ... -

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Basic information

Entry
Database: PDB / ID: 3ukl
TitleCrystal structure of UDP-galactopyranose mutase from Aspergillus fumigatus in complex with UDP
ComponentsUDP-galactopyranose mutase
KeywordsISOMERASE / FLAVOENZYME / FAD / UDP
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 / URIDINE-5'-DIPHOSPHATE / UDP-galactopyranose mutase
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 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)465,33232
Polymers455,5308
Non-polymers9,80124
Water18,7181039
1
A: UDP-galactopyranose mutase
B: UDP-galactopyranose mutase
D: UDP-galactopyranose mutase
F: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,70117
Polymers227,7654
Non-polymers4,93613
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18230 Å2
ΔGint-162 kcal/mol
Surface area76360 Å2
MethodPISA
2
C: UDP-galactopyranose mutase
E: UDP-galactopyranose mutase
hetero molecules

G: UDP-galactopyranose mutase
H: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,63015
Polymers227,7654
Non-polymers4,86511
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area17840 Å2
ΔGint-135 kcal/mol
Surface area76550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.440, 129.200, 172.820
Angle α, β, γ (deg.)90.07, 84.22, 82.24
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 2:511 ) 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)
511chain E and (resseq 2:511 ) and (not element H) and (not element D)
611chain F and (resseq 2:511 ) and (not element H) and (not element D)
711chain G and (resseq 2:511 ) and (not element H) and (not element D)
811chain H and (resseq 2:511 ) and (not element H) and (not element D)

NCS oper:
IDCodeMatrixVector
1given(-0.97909, 0.001222, 0.203423), (-0.081816, -0.917906, -0.388271), (0.186248, -0.396795, 0.898813)36.9006, 61.178799, 9.11182
2given(-0.964122, 0.264699, -0.020057), (0.264773, 0.96431, -0.00109), (0.019052, -0.006361, -0.999798)-15.2679, -63.385899, -35.451302
3given(0.941516, -0.25481, -0.220497), (-0.254864, -0.966551, 0.028701), (-0.220435, 0.029174, -0.974965)12.8746, 56.563202, 49.7225
4given(0.999941, 0.001828, 0.010696), (0.002285, 0.928161, -0.372172), (-0.010608, 0.372174, 0.928102)31.639099, -84.802498, 42.956402
5given(-0.96516, 0.260191, 0.027679), (0.25194, 0.895533, 0.366806), (0.070653, 0.360999, -0.929886)33.7286, -11.1292, 34.1022
6given(0.947826, -0.2633, -0.179721), (-0.178165, -0.905015, 0.38627), (-0.264355, -0.334096, -0.904708)27.814699, 15.1245, -48.5065
7given(-0.978944, 0.003155, 0.204106), (-0.009579, -0.999489, -0.03049), (0.203905, -0.031803, 0.978474)6.53731, -8.02302, 86.226898

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Components

#1: Protein
UDP-galactopyranose mutase /


Mass: 56941.309 Da / Num. of mol.: 8
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-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1039 / 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: 3.45 Å3/Da / Density % sol: 64.36 %
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: Dec 16, 2010 / 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: 2.63→48 Å / Num. all: 338440 / Num. obs: 165288 / % possible obs: 91.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 11.18
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.63-2.70.5351.55179.9
2.7-2.770.5041.7182.2
2.77-2.850.3862.2184
2.85-2.940.3182.68186.4
2.94-3.040.2393.56187.4
3.04-3.140.2094.15190.1
3.14-3.260.155.65191.7
3.26-3.40.1237.02193.4
3.4-3.550.0929.06194.5
3.55-3.720.07311.46195.4
3.72-3.920.05814.08195.6
3.92-4.160.04916.58196.7
4.16-4.450.03920.08197.3
4.45-4.80.03521.87197.2
4.8-5.260.03621.86197.4
5.26-5.880.03719.92198.5
5.88-6.790.03520.93198.7
6.79-8.320.02726.58198.4
8.32-11.760.01641.34198.5
11.76-480.01446.93195.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
MxDCdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: reduced AfUGM:UDPgalp complex structure

Resolution: 2.63→48 Å / Occupancy max: 1 / Occupancy min: 0.43 / SU ML: 0.79 / Isotropic thermal model: Isotropic / σ(F): 1.99 / Phase error: 24.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2314 8263 5 %
Rwork0.1846 --
obs0.187 165250 91.3 %
all-338440 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.429 Å2 / ksol: 0.326 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.4989 Å2-7.8223 Å21.4018 Å2
2---2.8077 Å2-2.2555 Å2
3----1.2751 Å2
Refinement stepCycle: LAST / Resolution: 2.63→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32032 0 632 1039 33703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00433546
X-RAY DIFFRACTIONf_angle_d0.77645712
X-RAY DIFFRACTIONf_dihedral_angle_d17.52712846
X-RAY DIFFRACTIONf_chiral_restr0.0514940
X-RAY DIFFRACTIONf_plane_restr0.0035844
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3993X-RAY DIFFRACTIONPOSITIONAL
12B3993X-RAY DIFFRACTIONPOSITIONAL0.199
13C3993X-RAY DIFFRACTIONPOSITIONAL0.181
14D4004X-RAY DIFFRACTIONPOSITIONAL0.187
15E3993X-RAY DIFFRACTIONPOSITIONAL0.197
16F4004X-RAY DIFFRACTIONPOSITIONAL0.188
17G4004X-RAY DIFFRACTIONPOSITIONAL0.183
18H3993X-RAY DIFFRACTIONPOSITIONAL0.17
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.63-2.7240.36027260.301513773X-RAY DIFFRACTION80
2.724-2.8330.34277560.286814371X-RAY DIFFRACTION84
2.833-2.9620.31467780.258914773X-RAY DIFFRACTION86
2.962-3.11810.30828060.240315332X-RAY DIFFRACTION89
3.1181-3.31340.28198300.21915768X-RAY DIFFRACTION92
3.3134-3.56920.25638520.204316202X-RAY DIFFRACTION94
3.5692-3.92820.2248650.174816425X-RAY DIFFRACTION96
3.9282-4.49620.18478780.136516678X-RAY DIFFRACTION97
4.4962-5.66340.16888820.128916758X-RAY DIFFRACTION98
5.6634-48.04090.18268900.157616907X-RAY DIFFRACTION98

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