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- PDB-2c5e: gdp-mannose-3', 5' -epimerase (arabidopsis thaliana), k217a, with... -

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Basic information

Entry
Database: PDB / ID: 2c5e
Titlegdp-mannose-3', 5' -epimerase (arabidopsis thaliana), k217a, with gdp-alpha-d-mannose 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 / 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-ALPHA-D-MANNOSE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / GDP-mannose 3,5-epimerase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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)88,76916
Polymers85,7712
Non-polymers2,99814
Water15,673870
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)62.481, 83.617, 66.232
Angle α, β, γ (deg.)90.00, 99.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 42885.500 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: GDP-ALPHA-D-MANNOSE WAS REFINED USING GMP (DEFINED AS GDP, MODIFIED IN THE CIF FILE TO REMOVE THE SECOND PHOSPHATE GROUP) AND MANNOSE-MONOPHOSPHATE (MA7), LINKING THE GDP O3A TO THE MA7 PB
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: PHISTEV-GME-K217A / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q93VR3, GDP-mannose 3,5-epimerase
#2: Chemical ChemComp-GDD / GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE


Mass: 605.341 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25N5O16P2
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 870 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYZES A REVERSIBLE EPIMERIZATION OF GDP-D-MANNOSE. ENGINEERED RESIDUE IN CHAIN A, LYS 217 TO ...CATALYZES A REVERSIBLE EPIMERIZATION OF GDP-D-MANNOSE. ENGINEERED RESIDUE IN CHAIN A, LYS 217 TO ALA ENGINEERED RESIDUE IN CHAIN B, LYS 217 TO ALA
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: 1.75 Å3/Da / Density % sol: 29.21 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6
Details: 100 MM BIS-TRIS PH 6.0, 2.2 M AMMONIUM SULPHATE. SITTING DROP, VAPOUR DIFFUSION. CRYOPTROTECTED WITH 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: 1.7→35.22 Å / Num. obs: 73777 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.2
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.2 / % possible all: 99.7

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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: 1.7→34.61 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.557 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.105 / Stereochemistry target values: RESTRAINED
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. EACH MONOMER OF GME K217A CONTAINS COMPOUNDS IN THE ACTIVE SITE NAD IN THE NUCLEOTIDE BINDING SITE, GDP- ALPHA-D- MANNOSE IN THE NUCLEOTIDE SUGAR BINDING SITE.
RfactorNum. reflection% reflectionSelection details
Rfree0.193 3705 5.04 %RANDOM
Rwork0.131 ---
obs0.134 73742 99.8 %-
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: 16.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.624 Å20 Å2-0.273 Å2
2--1.25 Å20 Å2
3----0.711 Å2
Refinement stepCycle: LAST / Resolution: 1.7→34.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5776 0 196 870 6842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0226261
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7351.9798484
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4945768
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.17124.178304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.304151101
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8181540
X-RAY DIFFRACTIONr_chiral_restr0.120.2887
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024768
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.23320
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.24194
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2801
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.271
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.259
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5561.53785
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.07925895
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.19432871
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4124.52567
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: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 263 -
Rwork0.179 5165 -
obs--99.67 %

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