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- PDB-1mv8: 1.55 A crystal structure of a ternary complex of GDP-mannose dehy... -

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Basic information

Entry
Database: PDB / ID: 1mv8
Title1.55 A crystal structure of a ternary complex of GDP-mannose dehydrogenase from Psuedomonas aeruginosa
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 / ACETIC ACID / Chem-GDX / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / GDP-mannose 6-dehydrogenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.55 Å
AuthorsSnook, C.F. / Tipton, P.A. / Beamer, L.J.
Citation
Journal: Biochemistry / Year: 2003
Title: The crystal structure of GDP-mannose dehydrogenase: A key enzyme in alginate biosynthesis of 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: Advisory / Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
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 2.1Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)196,68017
Polymers190,6264
Non-polymers6,05413
Water24,7891376
1
A: GDP-mannose 6-dehydrogenase
B: GDP-mannose 6-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2217
Polymers95,3132
Non-polymers2,9085
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16930 Å2
ΔGint-109 kcal/mol
Surface area29720 Å2
MethodPISA
2
C: GDP-mannose 6-dehydrogenase
D: GDP-mannose 6-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,45910
Polymers95,3132
Non-polymers3,1468
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16830 Å2
ΔGint-115 kcal/mol
Surface area30340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.472, 82.472, 309.893
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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Protein / Sugars , 2 types, 6 molecules ABCD

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


Mass: 47656.422 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.: 2
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

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Non-polymers , 5 types, 1387 molecules

#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 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: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1376 / 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: 2.76 Å3/Da / Density % sol: 55.49 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.6
Details: 8%v/v methyl propane diol, 0.1M Na Acetate, 1mM DTT, pH 4.6, VAPOR DIFFUSION, HANGING DROP
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
48. %MPD1reservoir
50.1 Msodium acetate1reservoirpH4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: SBC-2 / Detector: CCD / Date: Feb 8, 2001 / Details: Rosenbaum-Rock monochromator
RadiationMonochromator: Rosenbaum-Rock monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.55→40 Å / Num. obs: 294277 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 9.1
Reflection shellResolution: 1.55→1.61 Å / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 2.1 / Num. unique all: 28757 / % possible all: 97
Reflection
*PLUS
Num. measured all: 1557003
Reflection shell
*PLUS
% possible obs: 97 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1MUU

1muu


Resolution: 1.55→40 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.847 / SU ML: 0.096 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.072 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19441 14342 5.1 %RANDOM
Rwork0.17434 ---
all0.17535 ---
obs0.1753 269565 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 9.287 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2--0.12 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.55→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13141 0 362 1376 14879
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02113741
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212574
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.99918699
X-RAY DIFFRACTIONr_angle_other_deg0.742329191
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.81631740
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.173152368
X-RAY DIFFRACTIONr_chiral_restr0.0740.22218
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215099
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022607
X-RAY DIFFRACTIONr_nbd_refined0.2250.32961
X-RAY DIFFRACTIONr_nbd_other0.1960.312237
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.51245
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.4770.57
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3360.324
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2380.346
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.534
X-RAY DIFFRACTIONr_mcbond_it0.451.58628
X-RAY DIFFRACTIONr_mcangle_it0.834213882
X-RAY DIFFRACTIONr_scbond_it1.57135113
X-RAY DIFFRACTIONr_scangle_it2.5234.54817
LS refinement shellResolution: 1.55→1.591 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.266 1025
Rwork0.251 19437
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3682-0.02850.08060.2249-0.07250.25280.00580.06840.066-0.04930.0310.0014-0.00120.0365-0.03680.0753-0.00890.0050.12930.02490.1014-27.29495.1333-29.2433
20.268-0.01260.04110.19860.07620.3202-0.0039-0.02120.04480.03360.04440.0074-0.0135-0.0044-0.04060.07080.00970.00650.11480.0040.1022-31.60815.9149-4.3399
30.18990.0235-0.13460.1786-0.08130.2837-0.001-0.0169-0.01770.04370.0262-0.00260.00910.0314-0.02520.07820.0087-0.00230.13080.00560.086-28.899-34.9367-2.8381
40.1393-0.0175-0.08880.15410.05280.2817-0.00030.0021-0.021-0.02240.02060.00660.0197-0.017-0.02030.0746-0.006-0.0020.12360.00620.0944-33.2488-35.8995-27.967
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 4361 - 436
2X-RAY DIFFRACTION2BB1 - 4361 - 436
3X-RAY DIFFRACTION3CC1 - 4361 - 436
4X-RAY DIFFRACTION4DD1 - 4361 - 436
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.55 Å / Lowest resolution: 40 Å / % reflection Rfree: 5 % / Rfactor obs: 0.175 / Rfactor Rfree: 0.194 / Rfactor Rwork: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.4

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