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- PDB-2c5a: GDP-mannose-3', 5' -epimerase (Arabidopsis thaliana),Y174F, with ... -

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Basic information

Entry
Database: PDB / ID: 2c5a
TitleGDP-mannose-3', 5' -epimerase (Arabidopsis thaliana),Y174F, with GDP-beta-L-galactose bound in the active site
ComponentsGDP-MANNOSE-3', 5'-EPIMERASE
KeywordsISOMERASE / 3' 5'-EPIMERASE / SHORT CHAIN DEHYDRATASE/REDUCTASE / GDP-MANNOSE / GDP-GULOSE / GDP-GALACTOSE / KETO INTERMEDIATE / VITAMIN C / SDR / ASCORBATE BIOSYNTHESIS / NAD
Function / homology
Function and homology information


GDP-mannose 3,5-epimerase / GDP-mannose 3,5-epimerase activity / L-ascorbic acid biosynthetic process / plastid / NAD binding / cytosol
Similarity search - Function
GDP-mannose 3,5-epimerase / 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
FORMIC ACID / GUANOSINE-5'-DIPHOSPHATE-BETA-L-GALACTOSE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / GDP-mannose 3,5-epimerase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMajor, L.L. / Wolucka, B.A. / Naismith, J.H.
CitationJournal: J.Am.Chem.Soc. / Year: 2005
Title: Structure and Function of Gdp-Mannose-3',5'-Epimerase: An Enzyme which Performs Three Chemical Reactions at the Same Active Site.
Authors: Major, L.L. / Wolucka, B.A. / Naismith, J.H.
History
DepositionOct 26, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GDP-MANNOSE-3', 5'-EPIMERASE
B: GDP-MANNOSE-3', 5'-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,38424
Polymers85,8552
Non-polymers3,52922
Water18,3391018
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)62.497, 83.273, 66.120
Angle α, β, γ (deg.)90.00, 98.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein GDP-MANNOSE-3', 5'-EPIMERASE / GDP-MAN 3 / 5-EPIMERASE


Mass: 42927.602 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: GDP-BETA-L-GALACTOSE WAS REFINED USING GMP (DEFINED AS GDP, MODIFIED IN THE CIF FILE TO REMOVE THE SECOND PHOSPHATE GROUP) AND GALACTOSE-MONOPHOSPHATE (GA3), LINKING THE GDP O3A TO THE GA3 PB
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: PHISTEV-GME-Y174F / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q93VR3, GDP-mannose 3,5-epimerase

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Non-polymers , 5 types, 1040 molecules

#2: Chemical ChemComp-GDC / GUANOSINE-5'-DIPHOSPHATE-BETA-L-GALACTOSE


Mass: 605.341 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25N5O16P2
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1018 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCATALYZES A REVERSIBLE EPIMERIZATION OF GDP-D-MANNOSE ENGINEERED RESIDUE IN CHAIN A, TYR 174 TO PHE ...CATALYZES A REVERSIBLE EPIMERIZATION OF GDP-D-MANNOSE ENGINEERED RESIDUE IN CHAIN A, TYR 174 TO PHE ENGINEERED RESIDUE IN CHAIN B, TYR 174 TO PHE
Sequence detailsTHE FIRST TWO RESIDUES (GA) IN THE SPECIFIED SEQUENCE ARE A REMNANT FROM A CLEAVED HIS-TAG (AND ARE ...THE FIRST TWO RESIDUES (GA) IN THE SPECIFIED SEQUENCE ARE A REMNANT FROM A CLEAVED HIS-TAG (AND ARE NOT IN THE UNIPROT SEQUENCE), THE RESIDUE NUMBERING IN THE STRUCTURE USES THE THIRD RESIDUE (M) AS RESIDUE 1.

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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: 1.99 Å3/Da / Density % sol: 38.16 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6
Details: 100 MM BIS-TRIS PH 6.0, 2.2M AMMONIUM SULPHATE, SITTING DROP, VAPOUR DIFFUSION. CRYOPROTECTED 6 M SODIUM FORMATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: May 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.4→23.12 Å / Num. obs: 126826 / % possible obs: 96.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 11 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.9
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 5.5 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C54

2c54


Resolution: 1.4→21.61 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.472 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.049 / Stereochemistry target values: RESTRAINED
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. EACH MONOMER OF GME Y174F CONTAINS A NAD IN THE NUCLEOTIDE BINDING SITE, AND GDP-BETA-L-GALACTOSE IN THE NUCLEOTIDE SUGAR BINDING SITE.
RfactorNum. reflection% reflectionSelection details
Rfree0.14 6337 5.08 %RANDOM
Rwork0.103 ---
obs0.105 126798 96.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 9.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.262 Å20 Å2-0.05 Å2
2--0.589 Å20 Å2
3----0.342 Å2
Refinement stepCycle: LAST / Resolution: 1.4→21.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5786 0 231 1018 7035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0226384
X-RAY DIFFRACTIONr_bond_other_d0.0020.024430
X-RAY DIFFRACTIONr_angle_refined_deg1.9211.9848648
X-RAY DIFFRACTIONr_angle_other_deg1.086310779
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4075794
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.50924.248306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.532151144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3281539
X-RAY DIFFRACTIONr_chiral_restr0.2170.2905
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027050
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021305
X-RAY DIFFRACTIONr_nbd_refined0.230.21352
X-RAY DIFFRACTIONr_nbd_other0.2080.25151
X-RAY DIFFRACTIONr_nbtor_refined0.1860.23068
X-RAY DIFFRACTIONr_nbtor_other0.0890.23312
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2270.2844
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2830.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.291
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1881.54875
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.51825993
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.67333119
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7744.52621
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.189 459 -
Rwork0.11 8714 -
obs--95 %

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