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- PDB-5in5: Crystal Structure of GDP-mannose 4,6 dehydratase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5in5
TitleCrystal Structure of GDP-mannose 4,6 dehydratase in complex with natural inhibitor GDP-Fucose
ComponentsGDP-mannose 4,6 dehydratase
KeywordsLYASE/INHIBITOR / GDP-mannose 4 / 6 dehydratase / fucosylation / LYASE-INHIBITOR complex
Function / homology
Function and homology information


GDP-fucose biosynthesis / GDP-mannose 4,6-dehydratase / GDP-mannose 4,6-dehydratase activity / GDP-mannose metabolic process / 'de novo' GDP-L-fucose biosynthetic process / NADP+ binding / Notch signaling pathway / extracellular exosome / identical protein binding / cytoplasm / cytosol
Similarity search - Function
GDP-mannose 4,6-dehydratase / GDP-mannose 4,6 dehydratase / NAD(P)-binding domain / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / 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
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / GDP-mannose 4,6 dehydratase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsSickmier, E.A.
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Facile Modulation of Antibody Fucosylation with Small Molecule Fucostatin Inhibitors and Cocrystal Structure with GDP-Mannose 4,6-Dehydratase.
Authors: Allen, J.G. / Mujacic, M. / Frohn, M.J. / Pickrell, A.J. / Kodama, P. / Bagal, D. / San Miguel, T. / Sickmier, E.A. / Osgood, S. / Swietlow, A. / Li, V. / Jordan, J.B. / Kim, K.W. / ...Authors: Allen, J.G. / Mujacic, M. / Frohn, M.J. / Pickrell, A.J. / Kodama, P. / Bagal, D. / San Miguel, T. / Sickmier, E.A. / Osgood, S. / Swietlow, A. / Li, V. / Jordan, J.B. / Kim, K.W. / Rousseau, A.C. / Kim, Y.J. / Caille, S. / Achmatowicz, M. / Thiel, O. / Fotsch, C.H. / Reddy, P. / McCarter, J.D.
History
DepositionMar 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GDP-mannose 4,6 dehydratase
B: GDP-mannose 4,6 dehydratase
C: GDP-mannose 4,6 dehydratase
D: GDP-mannose 4,6 dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,79717
Polymers166,6014
Non-polymers7,19613
Water27,0951504
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22710 Å2
ΔGint-88 kcal/mol
Surface area45380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.137, 140.164, 86.028
Angle α, β, γ (deg.)90.000, 106.320, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
GDP-mannose 4,6 dehydratase / GDP-D-mannose dehydratase / GMD


Mass: 41650.168 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GMDS / Production host: Escherichia coli (E. coli) / References: UniProt: O60547, GDP-mannose 4,6-dehydratase

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Non-polymers , 5 types, 1517 molecules

#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical
ChemComp-GFB / GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE


Mass: 589.342 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H25N5O15P2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1504 / 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: 2.19 Å3/Da / Density % sol: 43.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES pH5.0, 10% PEG 6000, a final cryoprotectant containing 0.1 M MES pH5.0, 10% PEG6K, 20% glycerol

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 107619 / % possible obs: 94.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 18.51 Å2 / Rmerge(I) obs: 0.115 / Χ2: 1.658 / Net I/av σ(I): 13.331 / Net I/σ(I): 7.5 / Num. measured all: 388629
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.9-1.973.30.609191.3
1.97-2.053.40.446192.4
2.05-2.143.40.352193
2.14-2.253.50.274193.7
2.25-2.393.50.234194.3
2.39-2.583.60.191195.2
2.58-2.843.80.153196
2.84-3.253.90.106196.7
3.25-4.083.90.065197.6
4.08-203.80.052198.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIX1.10_2142refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 1.9→19.888 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.41
RfactorNum. reflection% reflection
Rfree0.1975 5383 5.01 %
Rwork0.1492 --
obs0.1516 107532 94.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 80.4 Å2 / Biso mean: 20.918 Å2 / Biso min: 7.72 Å2
Refinement stepCycle: final / Resolution: 1.9→19.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11288 0 462 1504 13254
Biso mean--16.44 30.26 -
Num. residues----1408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712072
X-RAY DIFFRACTIONf_angle_d0.92516445
X-RAY DIFFRACTIONf_chiral_restr0.0521792
X-RAY DIFFRACTIONf_plane_restr0.0052052
X-RAY DIFFRACTIONf_dihedral_angle_d18.9936979
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.893-1.91450.32181420.27112948309081
1.9145-1.9370.29781910.24793220341191
1.937-1.96060.26331760.23093326350292
1.9606-1.98540.29251830.20663298348192
1.9854-2.01150.24761760.19133304348093
2.0115-2.0390.25551610.1893355351692
2.039-2.06810.24321780.18523303348192
2.0681-2.0990.24471680.1783383355193
2.099-2.13170.20791810.1693313349493
2.1317-2.16660.25022010.16783354355594
2.1666-2.2040.23021800.16963344352494
2.204-2.2440.22451700.15953400357094
2.244-2.28710.20451690.15813388355794
2.2871-2.33370.22251930.15553414360794
2.3337-2.38440.22731830.15893373355695
2.3844-2.43970.22981920.15583407359995
2.4397-2.50060.21351780.15033394357295
2.5006-2.56810.18991670.15493467363495
2.5681-2.64350.22051880.15393436362496
2.6435-2.72860.24091760.15163470364696
2.7286-2.82590.18641860.14833428361496
2.8259-2.93870.20311820.14473493367596
2.9387-3.0720.19771760.14263513368997
3.072-3.23330.19341930.14183479367297
3.2333-3.43490.1611520.13843557370997
3.4349-3.69860.18531760.1253535371198
3.6986-4.06790.16342050.12843505371098
4.0679-4.64990.142010.10933521372298
4.6499-5.83380.14971760.12883594377098
5.8338-19.88920.14511830.12983627381099

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