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- PDB-5jnm: Crystal structure of MtlD from Staphylococcus aureus at 1.7-Angst... -

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Basic information

Entry
Database: PDB / ID: 5jnm
TitleCrystal structure of MtlD from Staphylococcus aureus at 1.7-Angstrom resolution
ComponentsMannitol-1-phosphate 5-dehydrogenase
KeywordsOXIDOREDUCTASE / mannitol-1-phosphate fructose-6-phosphate NAD dehydrogenase
Function / homology
Function and homology information


mannitol-1-phosphate 5-dehydrogenase / mannitol-1-phosphate 5-dehydrogenase activity / mannitol metabolic process
Similarity search - Function
Mannitol-1-phosphate 5-dehydrogenase / 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 ...Mannitol-1-phosphate 5-dehydrogenase / 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
Mannitol-1-phosphate 5-dehydrogenase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.701 Å
AuthorsTa, H.M. / Nguyen, T. / Kim, T. / Kim, K.K.
CitationJournal: Mbio / Year: 2019
Title: Targeting Mannitol Metabolism as an Alternative Antimicrobial Strategy Based on the Structure-Function Study of Mannitol-1-Phosphate Dehydrogenase in Staphylococcus aureus.
Authors: Nguyen, T. / Kim, T. / Ta, H.M. / Yeo, W.S. / Choi, J. / Mizar, P. / Lee, S.S. / Bae, T. / Chaurasia, A.K. / Kim, K.K.
History
DepositionApr 30, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mannitol-1-phosphate 5-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2114
Polymers44,9231
Non-polymers2883
Water8,215456
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.655, 58.105, 126.814
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Mannitol-1-phosphate 5-dehydrogenase /


Mass: 44922.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain Mu3 / ATCC 700698) (bacteria)
Strain: Mu3 / ATCC 700698 / Gene: mtlD, SAHV_2143 / Production host: Escherichia coli (E. coli)
References: UniProt: A7X522, mannitol-1-phosphate 5-dehydrogenase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 456 / 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: 2.47 Å3/Da / Density % sol: 50.25 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.8M Ammonium sulfate, 0.1M Cacodylate pH 6.5, 0.01M Cobalt(II) chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 46251 / % possible obs: 98.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.074 / Net I/av σ(I): 32.667 / Net I/σ(I): 8.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.7-1.766.10.428195.5
1.76-1.836.60.348197.3
1.83-1.916.80.271198.7
1.91-2.026.80.196198.9
2.02-2.1470.137199.2
2.14-2.3170.113199.4
2.31-2.5470.086199.7
2.54-2.9170.067199.8
2.91-3.6670.05199.9
3.66-506.80.053199.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.701→29.268 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.83
RfactorNum. reflection% reflection
Rfree0.1915 1989 4.31 %
Rwork0.1655 --
obs0.1667 46169 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.59 Å2 / Biso mean: 24.1262 Å2 / Biso min: 10.9 Å2
Refinement stepCycle: final / Resolution: 1.701→29.268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2962 0 15 456 3433
Biso mean--44.46 36.46 -
Num. residues----377
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043127
X-RAY DIFFRACTIONf_angle_d0.6444263
X-RAY DIFFRACTIONf_chiral_restr0.048486
X-RAY DIFFRACTIONf_plane_restr0.004560
X-RAY DIFFRACTIONf_dihedral_angle_d14.1921148
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7009-1.74340.23341330.21272939307293
1.7434-1.79050.26231340.20353035316996
1.7905-1.84320.21821340.1873071320598
1.8432-1.90270.21151390.17873118325798
1.9027-1.97070.21811400.18063107324799
1.9707-2.04960.20561440.17083138328299
2.0496-2.14280.20631440.15993155329999
2.1428-2.25580.18391430.15893160330399
2.2558-2.3970.20841460.15931743320100
2.397-2.5820.20971430.161931703313100
2.582-2.84160.15521450.159432113356100
2.8416-3.25240.19281420.162532413383100
3.2524-4.09590.16321470.150132633410100
4.0959-29.27240.19031550.172333983553100

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