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- PDB-1n7g: Crystal Structure of the GDP-mannose 4,6-dehydratase ternary comp... -

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Basic information

Entry
Database: PDB / ID: 1n7g
TitleCrystal Structure of the GDP-mannose 4,6-dehydratase ternary complex with NADPH and GDP-rhamnose.
ComponentsGDP-D-mannose-4,6-dehydratase
KeywordsLYASE / Rossmann fold / SDR / short-chain dehydrogenase/reductase
Function / homology
Function and homology information


GDP-mannose 4,6-dehydratase / GDP-mannose 4,6-dehydratase activity / unidimensional cell growth / 'de novo' GDP-L-fucose biosynthetic process / GTP binding / 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-RHAMNOSE / Chem-NDP / GDP-mannose 4,6 dehydratase 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsMulichak, A.M. / Bonin, C.P. / Reiter, W.-D. / Garavito, R.M.
CitationJournal: Biochemistry / Year: 2002
Title: The structure of the MUR1 GDP-mannose 4,6-dehydratase from A. thaliana: Implications for ligand binding and specificity.
Authors: Mulichak, A.M. / Bonin, C.P. / Reiter, W.-D. / Garavito, R.M.
History
DepositionNov 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)177,08711
Polymers172,3374
Non-polymers4,7507
Water8,557475
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21230 Å2
ΔGint-60 kcal/mol
Surface area41890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.180, 119.010, 118.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is the homotetramer observed in the asymmetric unit.

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Components

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


Mass: 43084.305 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: mur1 / Plasmid: pet28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P93031, 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-GDR / GUANOSINE-5'-DIPHOSPHATE-RHAMNOSE


Type: RNA linking / Mass: 589.342 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H25N5O15P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / 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: 2.32 Å3/Da / Density % sol: 47.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: ammonium sulfate, PEG 400, imidazole buffer, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.1 Mammonium sulfate1reservoir
22-2.5 %(w/v)PEG4001reservoir
30.1 Mimidazole1reservoirpH6.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 76177 / Num. obs: 72438 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.038
Reflection shellResolution: 2.2→2.3 Å / Rsym value: 0.202 / % possible all: 78.5
Reflection
*PLUS
Num. obs: 76177 / % possible obs: 92 % / Rmerge(I) obs: 0.038
Reflection shell
*PLUS
% possible obs: 78 % / Rmerge(I) obs: 0.202

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: MISSING SIDE CHAIN ATOMS FOR RESIDUES LISTED IN REMARK 470 WERE UNOBSERVED AND WERE NOT REFINED.
RfactorNum. reflectionSelection details
Rfree0.247 3521 RANDOM
Rwork0.201 --
all0.215 72041 -
obs0.215 72041 -
Refine analyzeLuzzati coordinate error obs: 0.26 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10253 0 306 475 11034
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.148
X-RAY DIFFRACTIONc_dihedral_angle_d22.77
X-RAY DIFFRACTIONc_improper_angle_d0.836
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

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