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- PDB-2c54: gdp-mannose-3', 5' -epimerase (arabidopsis thaliana),k178r, with ... -

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Basic information

Entry
Database: PDB / ID: 2c54
Titlegdp-mannose-3', 5' -epimerase (arabidopsis thaliana),k178r, with gdp-beta-l-gulose and gdp-4-keto-beta-l-gulose bound in 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-4-KETO-BETA-L-GULOSE / GUANOSINE 5'-DIPHOSPHATE-BETA-L-GULOSE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / GDP-mannose 3,5-epimerase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 25, 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 1.4Dec 19, 2018Group: Data collection / Database references / Derived calculations
Category: citation / struct_conn
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.5Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.6May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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)90,75427
Polymers85,9432
Non-polymers4,81125
Water17,006944
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)62.278, 82.457, 65.875
Angle α, β, γ (deg.)90.00, 98.77, 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: 42971.613 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: GDP-BETA-L-GULOSE WAS REFINED USING GMP (DEFINED AS GDP, MODIFIED IN THE CIF FILE TO REMOVE THE SECOND PHOSPHATE GROUP) AND GULOSE-MONOPHOSPHATE (GUL), LINKING THE GDP O3A TO THE GUL PB. GDP- ...Details: GDP-BETA-L-GULOSE WAS REFINED USING GMP (DEFINED AS GDP, MODIFIED IN THE CIF FILE TO REMOVE THE SECOND PHOSPHATE GROUP) AND GULOSE-MONOPHOSPHATE (GUL), LINKING THE GDP O3A TO THE GUL PB. GDP-BETA-L-4-KETO-GULOSE WAS REFINED USING GMP (DEFINED AS GDP, MODIFIED IN THE CIF FILE TO REMOVE THE SECOND PHOSPHATE GROUP) AND 4-KETO-GULOSE- MONOPHOSPHATE (4KG), LINKING THE GDP O3A TO THE 4KG PB NAD WAS REFINED USING ADP AND A NICOTINAMIDE RING (NI3), LINKING THE ADP PB TO THE NI3 O5* NADH WAS REFINED USING ADP AND A SKEWED REDUCED NICOTINAMIDE RING (NDH), LINKING THE ADP PB TO THE NDH O5*
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: PHISTEV-GME-K178R / 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 , 6 types, 969 molecules

#2: Chemical ChemComp-GKE / GUANOSINE 5'-DIPHOSPHATE-BETA-L-GULOSE


Mass: 605.341 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25N5O16P2
#3: Chemical ChemComp-GKD / GUANOSINE 5'-DIPHOSPHATE-4-KETO-BETA-L-GULOSE


Mass: 603.325 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H23N5O16P2
#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: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 944 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 178 TO ARG ENGINEERED RESIDUE IN CHAIN B, LYS 178 TO ARG
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: 1.95 Å3/Da / Density % sol: 37 %
Description: INITIAL MODEL FOR MOLECULAR REPLACEMENT BY PHASER DETERMINED BY MAD OF SELENO-METHIONINE PROTEIN. DATA COLLECTED ON BM14, ANALYSED WITH SOLVE AND RESOLVE.
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.4
Details: PROTEIN CRYSTALISED IN 100MM HEPES PH 7.4, 2.16 M AMMONIUM SULPHATE, VAPOUR DIFFUSION, SITTING DROP. CRYOPROTECTED WITH 4M SODIUM FORMATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 13, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.5→23.3 Å / Num. obs: 105071 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 13.37 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.6
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→64.55 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.281 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0.96 / ESU R: 0.082 / ESU R Free: 0.069 / Stereochemistry target values: RESTRAINED
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. EACH MONOMER OF GME K178R CONTAINS A MIXTURE OF COMPOUNDS IN THE ACTIVE SITE -NAD AND NADH IN THE NUCLEOTIDE BINDING SITE, GDP-BETA-L- ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. EACH MONOMER OF GME K178R CONTAINS A MIXTURE OF COMPOUNDS IN THE ACTIVE SITE -NAD AND NADH IN THE NUCLEOTIDE BINDING SITE, GDP-BETA-L-GULOSE AND GDP-BETA-L-4- KETO-GULOSE IN THE NUCLEOTIDE SUGAR BINDING SITE. DURING REFINEMENT THE CONSTANT PORTION OF EACH MOLECULE (ADP FOR NAD, GMP FOR THE GDP-SUGARS, AS THE SECOND PHOSPHATE GROUP MOVES WITH DIFFERENT LIGANDS) WAS FIXED WITH OCCUPANCY OF 1 AND LINKED TO TWO VARIABLE PORTIONS WITH PARTIAL OCCUPANCY.
RfactorNum. reflection% reflectionSelection details
Rfree0.167 5247 5.05 %RANDOM
Rwork0.118 ---
obs0.121 105045 99.9 %-
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: 11.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.586 Å20 Å2-0.157 Å2
2--1.229 Å20 Å2
3----0.691 Å2
Refinement stepCycle: LAST / Resolution: 1.5→64.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5786 0 313 944 7043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0226448
X-RAY DIFFRACTIONr_bond_other_d0.0020.024480
X-RAY DIFFRACTIONr_angle_refined_deg1.9432.0018745
X-RAY DIFFRACTIONr_angle_other_deg1.1213.00310792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4425789
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.51224.045309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.658151140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2791543
X-RAY DIFFRACTIONr_chiral_restr0.1270.2917
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027087
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021332
X-RAY DIFFRACTIONr_nbd_refined0.2210.21318
X-RAY DIFFRACTIONr_nbd_other0.2110.25142
X-RAY DIFFRACTIONr_nbtor_refined0.1850.23094
X-RAY DIFFRACTIONr_nbtor_other0.090.23412
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.2714
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.241
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2750.294
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.260.275
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0641.54848
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.38825955
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.56333225
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5784.52756
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: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.214 374
Rwork0.104 7372

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