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- PDB-3ukk: Crystal structure of R182K-UDP-galactopuranose mutase from Asperg... -

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Basic information

Entry
Database: PDB / ID: 3ukk
TitleCrystal structure of R182K-UDP-galactopuranose mutase from Aspergillus fumigatus in complex with UDPgalp
ComponentsUDP-galactopyranose mutase
KeywordsISOMERASE / FLAVOENZYME / FAD / FADH2 ISOMERASE
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 / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / URIDINE-5'-DIPHOSPHATE / UDP-galactopyranose mutase
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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)236,25012
Polymers231,4854
Non-polymers4,7658
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18050 Å2
ΔGint-106 kcal/mol
Surface area77640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.660, 123.660, 156.370
Angle α, β, γ (deg.)90.00, 103.26, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 2:510 ) and (not element H) and (not element D)
211chain B and (resseq 2:510 ) and (not element H) and (not element D)
311chain C and (resseq 2:510 ) and (not element H) and (not element D)
411chain D and (resseq 2:510 ) and (not element H) and (not element D)

NCS oper:
IDCodeMatrixVector
1given(-0.867185, 0.178967, 0.464717), (-0.003958, -0.935638, 0.352938), (0.497971, 0.304223, 0.81208)41.1744, -81.7463, 3.98662
2given(0.871334, 0.004151, -0.490672), (0.013091, -0.999805, 0.01479), (-0.490515, -0.01931, -0.871219)22.4839, -71.163498, 83.045898
3given(-0.984709, -0.168807, 0.043041), (-0.174167, 0.94862, -0.264171), (0.003765, -0.267628, -0.963515)48.175598, 12.742, 63.521099

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Components

#1: Protein
UDP-galactopyranose mutase


Mass: 57871.305 Da / Num. of mol.: 4 / Mutation: R182K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Strain: CSB 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-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.87 Å3/Da / Density % sol: 57.18 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 8.5
Details: 0.1M Bis-Tris-Propane pH 7.5-8.5, 0.2-0.35M sodium citrate, 10-20% 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 16, 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: 2.7→48.1 Å / Num. all: 173167 / Num. obs: 67309 / % possible obs: 93.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 7.66
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.7-2.772.4220.8021.3196.2
2.77-2.852.4560.6641.74196
2.85-2.932.4920.5252.15196.4
2.93-3.022.5230.4262.68196.4
3.02-3.122.5580.343.27196
3.12-3.232.5890.2624.12196.1
3.23-3.352.6090.1925.32196.1
3.35-3.492.6090.1736.28194.5
3.49-3.642.6140.1526.76189.5
3.64-3.822.5120.1059.7186
3.82-4.022.5170.09410.57183.3
4.02-4.272.6480.07212.38193.9
4.27-4.562.6520.0614.23193.7
4.56-4.932.6710.05814.63193
4.93-5.42.6650.05714.65193.6
5.4-6.042.6710.05714.13193.3
6.04-6.972.7020.05115.18193.6
6.97-8.542.680.04317.23192.5
8.54-12.072.6730.03720.41191.5
12.07-48.12.6020.03720.58188.7

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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

Resolution: 2.75→47.987 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.76 / Isotropic thermal model: Isotropic / σ(F): 1.99 / Phase error: 23.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2409 3182 5 %
Rwork0.1831 --
obs0.1859 63619 93.43 %
all-173167 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.07 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.5517 Å2-0 Å2-2.5248 Å2
2--1.6632 Å20 Å2
3---4.585 Å2
Refinement stepCycle: LAST / Resolution: 2.75→47.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16165 0 312 172 16649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416910
X-RAY DIFFRACTIONf_angle_d0.75423039
X-RAY DIFFRACTIONf_dihedral_angle_d14.86466
X-RAY DIFFRACTIONf_chiral_restr0.0532485
X-RAY DIFFRACTIONf_plane_restr0.0082944
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3994X-RAY DIFFRACTIONPOSITIONAL
12B3994X-RAY DIFFRACTIONPOSITIONAL0.472
13C3994X-RAY DIFFRACTIONPOSITIONAL0.445
14D3994X-RAY DIFFRACTIONPOSITIONAL0.373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.84830.3333280.23536233X-RAY DIFFRACTION96
2.8483-2.96230.28553250.22126181X-RAY DIFFRACTION96
2.9623-3.09710.3033270.21326198X-RAY DIFFRACTION96
3.0971-3.26040.25953250.19476180X-RAY DIFFRACTION96
3.2604-3.46460.2423230.18296141X-RAY DIFFRACTION95
3.4646-3.7320.28862940.23375591X-RAY DIFFRACTION86
3.732-4.10740.26023010.20275719X-RAY DIFFRACTION89
4.1074-4.70130.18043180.13046039X-RAY DIFFRACTION94
4.7013-5.92140.20633200.14426075X-RAY DIFFRACTION93
5.9214-47.99470.2113210.17786080X-RAY DIFFRACTION92

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