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- PDB-3uka: CRYSTAL STRUCTURE OF UDP-galactopyranose mutase from Aspergillus ... -

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Basic information

Entry
Database: PDB / ID: 3uka
TitleCRYSTAL STRUCTURE OF UDP-galactopyranose mutase from Aspergillus fumigatus
ComponentsUDP-galactopyranose mutase
KeywordsISOMERASE / UDP-GALACTOPYRANOSE MUTASE / AFUGM / FLAVOENZYME / FAD
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 / UDP-galactopyranose mutase
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.64 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 1.4Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)233,0818
Polymers229,9394
Non-polymers3,1424
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14350 Å2
ΔGint-77 kcal/mol
Surface area80750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.830, 73.560, 116.010
Angle α, β, γ (deg.)102.02, 101.07, 91.11
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 2:201 or resseq 208:312 or resseq...
211chain B and (resseq 2:201 or resseq 208:312 or resseq...
311chain C and (resseq 2:201 or resseq 208:312 or resseq...
411chain D and (resseq 2:201 or resseq 208:312 or resseq...

NCS oper:
IDCodeMatrixVector
1given(-0.999955, 0.003604, 0.008732), (-0.00522, 0.559566, -0.828769), (-0.007873, -0.828778, -0.559522)92.424797, 4.52145, 7.82584
2given(0.969182, -0.114131, -0.218314), (-0.123014, -0.992024, -0.027493), (-0.213434, 0.053502, -0.975491)2.03359, 153.427002, -63.260101
3given(-0.971239, 0.099799, 0.216183), (0.130218, -0.537495, 0.833152), (0.199345, 0.837341, 0.509041)90.841698, 137.710999, -89.130898

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Components

#1: Protein
UDP-galactopyranose mutase /


Mass: 57484.684 Da / Num. of mol.: 4
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 / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 5.5
Details: 0.1M Bis-Tris pH 5.5, 0.2M MgCl2, 13% PEG 3350, 4% acetonitrile, microbatch, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97969 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 7, 2007 / Details: double crystal monochromator
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97969 Å / Relative weight: 1
ReflectionResolution: 2.42→19.9 Å / % possible obs: 94.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.153 / Rsym value: 0.153 / Net I/σ(I): 5.24
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.42-2.651.9470.6421.210.642185.1
2.65-2.931.9910.5071.620.507197.3
2.93-3.281.9890.3092.750.309197.6
3.28-3.721.9910.1545.20.154197.7
3.72-4.31.9930.0858.90.085198.1
4.3-5.11.9910.0612.160.06198.2
5.1-6.261.9880.06211.820.062198.5
6.26-8.121.9830.04914.40.049198
8.12-11.551.9760.02523.990.025198
11.55-19.91.9670.02428.810.024176.3

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Phasing

PhasingMethod: molecular replacement

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Processing

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

Resolution: 2.64→19.72 Å / Occupancy max: 1 / Occupancy min: 0.47 / SU ML: 0.86 / Isotropic thermal model: Isotropic / σ(F): 2.09 / Phase error: 27.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2674 3241 5.11 %
Rwork0.2062 --
obs0.2093 63418 97.88 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.65 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.7083 Å2-2.8483 Å2-0.5624 Å2
2--2.847 Å2-7.997 Å2
3----2.1387 Å2
Refinement stepCycle: LAST / Resolution: 2.64→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15925 0 212 355 16492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00216563
X-RAY DIFFRACTIONf_angle_d0.56922546
X-RAY DIFFRACTIONf_dihedral_angle_d12.3546184
X-RAY DIFFRACTIONf_chiral_restr0.042436
X-RAY DIFFRACTIONf_plane_restr0.0032901
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3942X-RAY DIFFRACTIONPOSITIONAL
12B3942X-RAY DIFFRACTIONPOSITIONAL0.378
13C3928X-RAY DIFFRACTIONPOSITIONAL0.529
14D3942X-RAY DIFFRACTIONPOSITIONAL0.568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.73410.36133050.29985960X-RAY DIFFRACTION97
2.7341-2.84330.34443150.26456023X-RAY DIFFRACTION97
2.8433-2.97230.34253220.25215932X-RAY DIFFRACTION97
2.9723-3.12840.32293410.24136025X-RAY DIFFRACTION98
3.1284-3.32360.30763330.21866055X-RAY DIFFRACTION98
3.3236-3.57880.26893190.19195964X-RAY DIFFRACTION98
3.5788-3.93630.25023290.17666048X-RAY DIFFRACTION98
3.9363-4.50.21063310.16456024X-RAY DIFFRACTION98
4.5-5.64740.22833310.17546068X-RAY DIFFRACTION98
5.6474-19.72010.23883150.21126078X-RAY DIFFRACTION99

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