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- PDB-1mfz: Partially refined 2.8 A Crystal structure of GDP-mannose dehydrog... -

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Basic information

Entry
Database: PDB / ID: 1mfz
TitlePartially refined 2.8 A Crystal structure of GDP-mannose dehydrogenase from P. 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
Chem-GDX / GDP-mannose 6-dehydrogenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 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
DepositionAug 14, 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 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / exptl_crystal_grow / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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 / _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp / _struct_conn.pdbx_leaving_atom_flag / _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-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)194,7918
Polymers192,3144
Non-polymers2,4774
Water1,910106
1
A: GDP-mannose 6-dehydrogenase
B: GDP-mannose 6-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3964
Polymers96,1572
Non-polymers1,2392
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14240 Å2
ΔGint-100 kcal/mol
Surface area30520 Å2
MethodPISA
2
C: GDP-mannose 6-dehydrogenase
D: GDP-mannose 6-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3964
Polymers96,1572
Non-polymers1,2392
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14070 Å2
ΔGint-99 kcal/mol
Surface area30860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.173, 136.834, 218.562
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.55 Å3/Da / Density % sol: 51.74 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.6
Details: 10% PEG 3350, 20% isopropanol, 0.1 M Na citrate, pH 5.6, 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
410 %PEG33501reservoir
520 %2-propanol1reservoir
60.1 Msodium citrate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: Osmic confocal
RadiationMonochromator: Osmic confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→94.691 Å / Num. obs: 48049 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 34.7 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.7
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 4.4 / Num. unique all: 4322 / % possible all: 90
Reflection
*PLUS
Num. measured all: 151736
Reflection shell
*PLUS
% possible obs: 90 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→40 Å / SU B: 14.6806 / SU ML: 0.30112 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.40486 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26325 2429 5.1 %RANDOM
Rwork0.20361 ---
all0.20656 ---
obs0.2065 45582 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 34.708 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2--1.09 Å20 Å2
3----1.33 Å2
Refinement stepCycle: LAST / Resolution: 2.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13017 0 160 106 13283
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.014
X-RAY DIFFRACTIONr_angle_refined_deg1.303
X-RAY DIFFRACTIONr_chiral_restr0.082
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.259
X-RAY DIFFRACTIONr_gen_planes_refined0.004
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0.35
RfactorNum. reflection% reflection
Rfree0.24 157 -
obs-2937 100 %
Refinement
*PLUS
Lowest resolution: 40 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.263 / Rfactor Rwork: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.3

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