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- PDB-1m2w: Pseudomonas fluorescens mannitol 2-dehydrogenase ternary complex ... -

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Basic information

Entry
Database: PDB / ID: 1m2w
TitlePseudomonas fluorescens mannitol 2-dehydrogenase ternary complex with NAD and D-mannitol
Componentsmannitol dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann fold / di-nucleotide binding motif / long-chain dehydrogenase / polyol dehydrogenase / secondary alcohol dehydrogenase
Function / homology
Function and homology information


mannitol 2-dehydrogenase / mannitol 2-dehydrogenase activity / mannitol metabolic process / nucleotide binding
Similarity search - Function
Mannitol dehydrogenase, conserved site / Mannitol dehydrogenases signature. / Mannitol dehydrogenase / Mannitol dehydrogenase, N-terminal / Mannitol dehydrogenase Rossmann domain / Mannitol dehydrogenase, C-terminal / Mannitol dehydrogenase C-terminal domain / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 ...Mannitol dehydrogenase, conserved site / Mannitol dehydrogenases signature. / Mannitol dehydrogenase / Mannitol dehydrogenase, N-terminal / Mannitol dehydrogenase Rossmann domain / Mannitol dehydrogenase, C-terminal / Mannitol dehydrogenase C-terminal domain / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
D-MANNITOL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Mannitol dehydrogenase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKavanagh, K.L. / Klimacek, M. / Nidetzky, B. / Wilson, D.K.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal Structure of Pseudomonas fluorescens Mannitol 2-Dehydrogenase Binary and Ternary Complexes. Specificity and Catalytic Mechanism
Authors: Kavanagh, K.L. / Klimacek, M. / Nidetzky, B. / Wilson, D.K.
History
DepositionJun 25, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mannitol dehydrogenase
B: mannitol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,8366
Polymers110,1452
Non-polymers1,6914
Water11,349630
1
A: mannitol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9183
Polymers55,0731
Non-polymers8462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: mannitol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9183
Polymers55,0731
Non-polymers8462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.954, 104.531, 101.505
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-5771-

HOH

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Components

#1: Protein mannitol dehydrogenase / / E.C.1.1.1.67


Mass: 55072.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: DSM50106 / Gene: mtlD / Production host: Escherichia coli (E. coli) / References: UniProt: O08355, mannitol 2-dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-MTL / D-MANNITOL / Mannitol


Mass: 182.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O6 / Comment: medication*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 630 / 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: 2.57 Å3/Da / Density % sol: 52.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 34% PEG 4000, 250 mM ammonium acetate, 100 mM sodium citrate, 10 mM DTT, pH 5.0, VAPOR DIFFUSION, HANGING DROP at 293K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
114 mg/mlprotein1drop
210 mMTris1drop
325 mM1droppH7.5NaCl
45 mMNADH1drop
530 %(w/v)PEG40001reservoir
6200 mMammonium acetate1reservoir
7100 mMsodium citrate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.9198 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 24, 2002
RadiationMonochromator: silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9198 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 105733 / Num. obs: 104464 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 18.4
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 2.8 / % possible all: 96.1
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 105300 / Num. measured all: 367595 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
Highest resolution: 1.8 Å / % possible obs: 96.1 % / Rmerge(I) obs: 0.371

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Processing

Software
NameVersionClassification
EPMRphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LJ8

1lj8


Resolution: 1.8→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.202 5257 -RANDOM
Rwork0.176 ---
all0.1761 105733 --
obs0.1761 104464 98.8 %-
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7658 0 112 630 8400
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.68
X-RAY DIFFRACTIONc_bond_d0.016
LS refinement shellResolution: 1.8→1.84 Å /
Num. reflection% reflection
obs6706 96.1 %
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 30 Å / Rfactor obs: 0.1761 / Rfactor Rfree: 0.202 / Rfactor Rwork: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS

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