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- PDB-1n7h: Crystal Structure of GDP-mannose 4,6-dehydratase ternary complex ... -

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Basic information

Entry
Database: PDB / ID: 1n7h
TitleCrystal Structure of GDP-mannose 4,6-dehydratase ternary complex with NADPH and GDP
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 / GDP-mannose metabolic process / 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 / Chem-NDP / GDP-mannose 4,6 dehydratase 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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: Derived calculations / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5466
Polymers86,1692
Non-polymers2,3774
Water7,927440
1
A: GDP-D-mannose-4,6-dehydratase
B: GDP-D-mannose-4,6-dehydratase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)177,09212
Polymers172,3374
Non-polymers4,7548
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area20910 Å2
ΔGint-53 kcal/mol
Surface area41700 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)116.860, 124.440, 110.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-675-

HOH

21A-792-

HOH

DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the transformation: -x+1, y, -z+1/2

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Components

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


Mass: 43084.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: mur1 / Plasmid: pet28b / Production host: Escherichia coli (E. coli) / References: UniProt: P93031, GDP-mannose 4,6-dehydratase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 2.45 Å3/Da / Density % sol: 49.42 %
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-ID
12 MNADPH1reservoir
210 mMGDP1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Oct 10, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→10 Å / Num. all: 70812 / Num. obs: 70104 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rsym value: 0.063
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4 % / Num. unique all: 6532 / Rsym value: 0.077 / % possible all: 88
Reflection
*PLUS
Lowest resolution: 10 Å / Num. obs: 70780 / % possible obs: 95 % / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 88 % / Rmerge(I) obs: 0.077

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→10 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Partial or no side chain atoms were refined for residues listed in REMARK 470.
RfactorNum. reflection% reflectionSelection details
Rfree0.2 3557 -RANDOM
Rwork0.181 ---
all0.182 69991 --
obs0.182 69991 94 %-
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5240 0 152 440 5832
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.38
X-RAY DIFFRACTIONc_dihedral_angle_d23.14
X-RAY DIFFRACTIONc_improper_angle_d1.02
LS refinement shellResolution: 1.8→1.86 Å
RfactorNum. reflection% reflection
Rfree0.215 312 -
Rwork0.19 --
obs-6443 86.9 %
Refinement
*PLUS
Lowest resolution: 10 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.201 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1

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