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- PDB-1t2a: Crystal structure of human GDP-D-mannose 4,6-dehydratase -

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Basic information

Entry
Database: PDB / ID: 1t2a
TitleCrystal structure of human GDP-D-mannose 4,6-dehydratase
ComponentsGDP-mannose 4,6 dehydratase
KeywordsSTRUCTURAL GENOMICS / LYASE / Structural Genomics Consortium / Rossman-fold / short-chain dehydrogenase/reductase / SDR
Function / homology
Function and homology information


GDP-L-fucose biosynthetic process / 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 ...GDP-L-fucose biosynthetic process / 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 / cytosol / cytoplasm
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 / Chem-NDP / GDP-mannose 4,6 dehydratase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsWalker, J.R. / Vedadi, M. / Sharma, S. / Houston, S. / Wasney, G. / Loppnau, P. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure and Biophysical Characterization of Human GDP-D-mannose 4,6-dehydratase
Authors: Vedadi, M. / Walker, J.R. / Sharma, S. / Houston, S. / Wasney, G. / Loppnau, P. / Oppermann, U.
History
DepositionApr 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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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)175,55212
Polymers170,7974
Non-polymers4,7548
Water17,979998
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19060 Å2
ΔGint-73 kcal/mol
Surface area45920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.595, 122.064, 139.403
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAINS. THIS REPRESENTS THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE.

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Components

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


Mass: 42699.266 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GMDS / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star / References: UniProt: O60547, GDP-mannose 4,6-dehydratase
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 998 / 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: 2.48 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 21% PEG 4000, 0.1 M Tris pH 8.5, 0.2 M sodium acetate, 0.075 M BOG, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979174 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Mar 12, 2004
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979174 Å / Relative weight: 1
ReflectionResolution: 1.84→25 Å / Num. all: 131584 / Num. obs: 129347 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 19.7
Reflection shellResolution: 1.84→1.91 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 2.81 / % possible all: 97.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N7H

1n7h


Resolution: 1.84→24.93 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3192953.56 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 6503 5 %RANDOM
Rwork0.173 ---
obs0.173 129250 98.2 %-
all-129250 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.1057 Å2 / ksol: 0.37589 e/Å3
Displacement parametersBiso mean: 24.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.96 Å20 Å20 Å2
2---2.2 Å20 Å2
3---5.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.84→24.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10864 0 304 998 12166
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.023
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_improper_angle_d0
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it22
X-RAY DIFFRACTIONc_scbond_it2.272
X-RAY DIFFRACTIONc_scangle_it3.352.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.261 692 4.9 %
Rwork0.222 13451 -
obs--61.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2GDP.PAR&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3NDP.PAR&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4WATER_REP.PARAM&_1_TOPOLOGY_INFILE_4

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