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- PDB-3aw9: Structure of UDP-galactose 4-epimerase mutant -

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Basic information

Entry
Database: PDB / ID: 3aw9
TitleStructure of UDP-galactose 4-epimerase mutant
ComponentsNAD-dependent epimerase/dehydratase
KeywordsISOMERASE / Rossmann fold
Function / homology
Function and homology information


UDP-glucose 4-epimerase activity / galactose catabolic process via UDP-galactose / oxidoreductase activity / nucleotide binding / cytosol
Similarity search - Function
UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold ...UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GALACTOSE-URIDINE-5'-DIPHOSPHATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD-dependent epimerase/dehydratase
Similarity search - Component
Biological speciesPyrobaculum calidifontis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsSakuraba, H. / Kawai, T. / Yoneda, K. / Ohshima, T.
CitationJournal: To be Published
Title: Structure of UDP-galactose 4-epimerase mutant
Authors: Sakuraba, H. / Kawai, T. / Yoneda, K. / Ohshima, T.
History
DepositionMar 15, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: NAD-dependent epimerase/dehydratase
B: NAD-dependent epimerase/dehydratase
C: NAD-dependent epimerase/dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,2849
Polymers101,5953
Non-polymers3,6896
Water4,666259
1
A: NAD-dependent epimerase/dehydratase
hetero molecules

A: NAD-dependent epimerase/dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1896
Polymers67,7302
Non-polymers2,4594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2370 Å2
ΔGint-27 kcal/mol
Surface area24330 Å2
MethodPISA
2
B: NAD-dependent epimerase/dehydratase
C: NAD-dependent epimerase/dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1896
Polymers67,7302
Non-polymers2,4594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-27 kcal/mol
Surface area24220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.623, 113.644, 217.267
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein NAD-dependent epimerase/dehydratase


Mass: 33864.934 Da / Num. of mol.: 3 / Mutation: DELETION MUTANT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum calidifontis (archaea) / Strain: JCM 11548 / VA1 / Gene: Pcal_0885 / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3MUJ4
#2: Chemical ChemComp-GDU / GALACTOSE-URIDINE-5'-DIPHOSPHATE / UDP-D-GALACTOPYRANOSE


Mass: 566.302 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C15H24N2O17P2
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDELETION MUTANT, UNP RESIDUES 32-43 (NLSSGRREFVNP) OF THE NAD-BINDING LOOP OF THE WILD TYPE WERE ...DELETION MUTANT, UNP RESIDUES 32-43 (NLSSGRREFVNP) OF THE NAD-BINDING LOOP OF THE WILD TYPE WERE REPLACED WITH RESIDUES 32-39 (IVQRDTGG)

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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: 2.69 Å3/Da / Density % sol: 54.31 %
Crystal growTemperature: 293 K / Method: sitting drop / pH: 8 / Details: PEG 8000, pH 8.0, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 26, 2010 / Details: Rhodium coated silicon single crystal
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→108.47 Å / Num. all: 48870 / Num. obs: 48870 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
DMphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 6.662 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2365 2467 5.1 %RANDOM
Rwork0.2045 ---
all0.2062 48870 --
obs0.2045 48765 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.45 Å2 / Biso mean: 34.6108 Å2 / Biso min: 10.76 Å2
Baniso -1Baniso -2Baniso -3
1-4.85 Å20 Å20 Å2
2---3.14 Å20 Å2
3----1.71 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7001 0 240 259 7500
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0227404
X-RAY DIFFRACTIONr_angle_refined_deg1.5022.00610111
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3655895
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.13222.947302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.996151174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5661560
X-RAY DIFFRACTIONr_chiral_restr0.090.21188
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025454
X-RAY DIFFRACTIONr_nbd_refined0.20.23443
X-RAY DIFFRACTIONr_nbtor_refined0.3060.24963
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2454
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1410.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.210
X-RAY DIFFRACTIONr_mcbond_it0.8211.54621
X-RAY DIFFRACTIONr_mcangle_it1.38627236
X-RAY DIFFRACTIONr_scbond_it1.84833237
X-RAY DIFFRACTIONr_scangle_it2.9064.52875
LS refinement shellResolution: 2.303→2.362 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 174 -
Rwork0.242 3336 -
all-3510 -
obs--98.71 %

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