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- PDB-1muu: 2.0 A crystal structure of GDP-mannose dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 1muu
Title2.0 A crystal structure of GDP-mannose dehydrogenase
ComponentsGDP-mannose 6-dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann fold / domain-swapped dimer / enzyme complex with cofactor and product
Function / homology
Function and homology information


GDP-mannose 6-dehydrogenase / GDP-mannose 6-dehydrogenase activity / alginic acid biosynthetic process / single-species biofilm formation / response to osmotic stress / cellular response to cell envelope stress / NAD binding
Similarity search - Function
GDP-mannose 6-dehydrogenase / UDP-glucose/GDP-mannose dehydrogenase, N-terminal / UDP-glucose/GDP-mannose dehydrogenase, dimerisation / UDP-glucose/GDP-mannose dehydrogenase, C-terminal / UDP-glucose/GDP-mannose dehydrogenase / UDP-glucose/GDP-mannose dehydrogenase, C-terminal domain superfamily / UDP-glucose/GDP-mannose dehydrogenase family, central domain / UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain / UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain / UDP binding domain ...GDP-mannose 6-dehydrogenase / UDP-glucose/GDP-mannose dehydrogenase, N-terminal / UDP-glucose/GDP-mannose dehydrogenase, dimerisation / UDP-glucose/GDP-mannose dehydrogenase, C-terminal / UDP-glucose/GDP-mannose dehydrogenase / UDP-glucose/GDP-mannose dehydrogenase, C-terminal domain superfamily / UDP-glucose/GDP-mannose dehydrogenase family, central domain / UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain / UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain / UDP binding domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
sucrose / Chem-GDX / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / GDP-mannose 6-dehydrogenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.02 Å
AuthorsSnook, C.F. / Tipton, P.A. / Beamer, L.J.
Citation
Journal: Biochemistry / Year: 2003
Title: Crystal structure of GDP-mannose dehydrogenase: A key enzyme of alginate biosynthesis in P. aeruginosa
Authors: Snook, C.F. / Tipton, P.A. / Beamer, L.J.
#1: Journal: Biochemistry / Year: 2002
Title: Allosterism and cooperativity in Pseudomonas aeruginosa GDP-mannose dehydrogenase
Authors: Naught, L.E. / Gilbert, S. / Imhoff, R. / Snook, C. / Beamer, L. / Tipton, P.
History
DepositionSep 24, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GDP-mannose 6-dehydrogenase
B: GDP-mannose 6-dehydrogenase
C: GDP-mannose 6-dehydrogenase
D: GDP-mannose 6-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,78713
Polymers192,3144
Non-polymers5,4739
Water16,268903
1
A: GDP-mannose 6-dehydrogenase
B: GDP-mannose 6-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,7226
Polymers96,1572
Non-polymers2,5664
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16220 Å2
ΔGint-112 kcal/mol
Surface area28920 Å2
MethodPISA
2
C: GDP-mannose 6-dehydrogenase
D: GDP-mannose 6-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,0657
Polymers96,1572
Non-polymers2,9085
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16530 Å2
ΔGint-112 kcal/mol
Surface area29610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.497, 82.497, 310.173
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
GDP-mannose 6-dehydrogenase / GMD


Mass: 48078.469 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: algD / Plasmid: pET-3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P11759, GDP-mannose 6-dehydrogenase
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-GDX / GUANOSINE 5'-(TRIHYDROGEN DIPHOSPHATE), P'-D-MANNOPYRANOSYL ESTER


Mass: 619.325 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H23N5O17P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 903 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.74 Å3/Da / Density % sol: 55.16 %
Crystal growTemperature: 323 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 8% MPD, 100 mM Na acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 323K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 mMHEPES1droppH7.5
21.0 mMdithiothreitol1drop
37.5 mg/mlprotein1drop
42 %PEG33501reservoir
520 mMmagnesium sulfate1reservoir
60.1 Msodium acetate1reservoirpH4.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934, 0.97947, 0.94225
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979341
20.979471
30.942251
ReflectionResolution: 2→50 Å / Num. all: 128981 / Num. obs: 128981 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.103 Å / % possible all: 90.2
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 129450 / % possible obs: 99.7 % / Num. measured all: 975001 / Rmerge(I) obs: 0.088
Reflection shell
*PLUS
% possible obs: 99.4 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
REFMAC5refinement
RefinementMethod to determine structure: MAD / Resolution: 2.02→50 Å / SU B: 5.66747 / SU ML: 0.15707 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.18769 / ESU R Free: 0.15821 / Stereochemistry target values: Engh & Huber / Details: TLS refinement with 4 chains in asu
RfactorNum. reflection% reflectionSelection details
Rfree0.23442 6829 5 %RANDOM
Rwork0.20872 ---
obs0.20999 128981 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 18.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refine analyzeLuzzati coordinate error obs: 0.2605 Å
Refinement stepCycle: LAST / Resolution: 2.02→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12856 0 323 903 14082
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.992
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3713
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.00715
X-RAY DIFFRACTIONr_chiral_restr0.080.2
X-RAY DIFFRACTIONr_gen_planes_refined
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.5341.5
X-RAY DIFFRACTIONr_mcangle_it1.0122
X-RAY DIFFRACTIONr_scbond_it1.7023
X-RAY DIFFRACTIONr_scangle_it2.7894.5
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.02→2.08 Å /
RfactorNum. reflection
Rfree0.24 457
Rwork0.21 -
obs-7911
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.234 / Rfactor Rwork: 0.209 / Highest resolution: 2.02 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.012
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.4

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