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- PDB-4lis: Crystal Structure of UDP-galactose-4-epimerase from Aspergillus n... -

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Basic information

Entry
Database: PDB / ID: 4lis
TitleCrystal Structure of UDP-galactose-4-epimerase from Aspergillus nidulans
ComponentsUDP-glucose 4-epimerase
KeywordsISOMERASE / Catalysis / Hydrogen Bonding / Kinetics / Binding Sites / Protein Structure
Function / homology
Function and homology information


monosaccharide metabolic process / UDP-glucose 4-epimerase / UDP-glucose 4-epimerase activity / galactose metabolic process / nucleotide binding / cytoplasm / cytosol
Similarity search - Function
UDP-glucose 4-epimerase / GDP-mannose 4,6 dehydratase / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold ...UDP-glucose 4-epimerase / GDP-mannose 4,6 dehydratase / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / 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
IODIDE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / URIDINE-5'-DIPHOSPHATE / URIDINE-5'-DIPHOSPHATE-GLUCOSE / UDP-glucose 4-epimerase
Similarity search - Component
Biological speciesAspergillus nidulans FGSC A4 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsDalrymple, S.A. / Ko, J. / Sheoran, I. / Kaminskyj, S.G.W. / Sanders, D.A.R.
CitationJournal: Plos One / Year: 2013
Title: Elucidation of Substrate Specificity in Aspergillus nidulans UDP-Galactose-4-Epimerase.
Authors: Dalrymple, S.A. / Ko, J. / Sheoran, I. / Kaminskyj, S.G. / Sanders, D.A.
History
DepositionJul 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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-glucose 4-epimerase
B: UDP-glucose 4-epimerase
C: UDP-glucose 4-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,41319
Polymers121,8143
Non-polymers4,59916
Water1,33374
1
A: UDP-glucose 4-epimerase
hetero molecules

A: UDP-glucose 4-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,61514
Polymers81,2102
Non-polymers3,40512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8320 Å2
ΔGint-42 kcal/mol
Surface area26930 Å2
MethodPISA
2
B: UDP-glucose 4-epimerase
C: UDP-glucose 4-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,10612
Polymers81,2102
Non-polymers2,89710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-39 kcal/mol
Surface area27270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.133, 119.154, 161.424
Angle α, β, γ (deg.)90.000, 98.480, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 4:365 )
21chain B and (resseq 4:365 )
31chain C and (resseq 4:365 )

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 4 - 365 / Label seq-ID: 4 - 365

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain 'A' and (resseq 4:365 )AA
2chain 'B' and (resseq 4:365 )BB
3chain 'C' and (resseq 4:365 )CC

NCS oper:
IDCodeMatrixVector
1given(0.492038, 0.840951, 0.225169), (0.840425, -0.526312, 0.129156), (0.227123, 0.125688, -0.965721)-16.368099, 14.8881, 51.904701
2given(-0.443124, -0.86882, -0.22089), (0.869067, -0.476785, 0.131904), (-0.219918, -0.133519, 0.966338)17.083401, 14.5536, -51.877602

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein UDP-glucose 4-epimerase


Mass: 40604.750 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus nidulans FGSC A4 (mold) / Strain: AAE1 / Gene: ANIA_04727, GALE / Plasmid: pHISTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-gold(DE3) / References: UniProt: C8VAU8

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Non-polymers , 6 types, 90 molecules

#2: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: I
#6: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.58 Å3/Da / Density % sol: 52.36 %
Crystal growTemperature: 278 K / Method: evaporation / pH: 7.5
Details: 20%(w/v) PEG 3350, 0.1M Bis-Tris propane, 0.2M NaF, microbatch, temperature 278K, pH 7.5, EVAPORATION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 3, 2010 / Details: double crystal monochromator
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→36.71 Å / Num. all: 30056 / Num. obs: 30056 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.09 % / Rmerge(I) obs: 0.131 / Χ2: 1.08 / Net I/σ(I): 8.1 / Scaling rejects: 17283
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.8-2.97.340.5143.22338029891.2298.5
2.9-3.027.30.4553.62340030051.298.7
3.02-3.157.30.3754.22344030001.1998.6
3.15-3.327.210.2815.32330630031.1698.7
3.32-3.537.140.2186.52326830091.1598.6
3.53-3.87.010.1638.12297030011.0898.6
3.8-4.186.920.13110.22292530071.0398.7
4.18-4.796.880.11511.92261730120.9698.4
4.79-6.026.990.10412.72281930180.998.5
6.02-36.716.840.08616.32230930120.8996.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.51 Å36.71 Å
Translation2.51 Å36.71 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.9.8.0Ldata scaling
d*TREK9.9.9.7Ldata reduction
MOLREPphasing
PHENIXdev_1327refinement
PDB_EXTRACT3.11data extraction
MxDCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1HZJ

1hzj


Resolution: 2.8→36.71 Å / Occupancy max: 1 / Occupancy min: 0.43 / FOM work R set: 0.7141 / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 34.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2616 1508 5.04 %RANDOM
Rwork0.2127 ---
obs0.2153 29919 97.96 %-
all-29919 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.33 Å2 / Biso mean: 70.9331 Å2 / Biso min: 21.26 Å2
Refinement stepCycle: LAST / Resolution: 2.8→36.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8399 0 233 74 8706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028853
X-RAY DIFFRACTIONf_angle_d0.55612098
X-RAY DIFFRACTIONf_chiral_restr0.041342
X-RAY DIFFRACTIONf_plane_restr0.0031555
X-RAY DIFFRACTIONf_dihedral_angle_d10.1783425
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2797X-RAY DIFFRACTIONPOSITIONAL0.293
12B2797X-RAY DIFFRACTIONPOSITIONAL0.293
13C2781X-RAY DIFFRACTIONPOSITIONAL0.271
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8001-2.89050.38271220.29942571269397
2.8905-2.99370.38891410.29322585272698
2.9937-3.11350.37011310.29472558268998
3.1135-3.25520.38121370.2662584272198
3.2552-3.42670.34651150.24232613272898
3.4267-3.64120.32571490.22272560270998
3.6412-3.9220.26161260.2022575270198
3.922-4.31610.21831520.18042583273599
4.3161-4.93940.20961430.17262588273198
4.9394-6.21820.20871440.19912616276098
6.2182-36.71570.22491480.19922578272696

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