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- PDB-3w6z: Crystal structure of NADP bound L-serine 3-dehydrogenase (K170M) ... -

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Basic information

Entry
Database: PDB / ID: 3w6z
TitleCrystal structure of NADP bound L-serine 3-dehydrogenase (K170M) from Hyperthermophilic Archaeon Pyrobaculum calidifontis
Components6-phosphogluconate dehydrogenase, NAD-binding protein
KeywordsOXIDOREDUCTASE / HYPERTHERMOPHILIC ARCHAEON / ROSSMANN FOLD / L-SERINE 3-DEHYDROGENASE / NAD(P) BINDING
Function / homology
Function and homology information


L-serine 3-dehydrogenase (NAD+) / NAD binding / NADP binding / oxidoreductase activity
Similarity search - Function
3-hydroxyisobutyrate dehydrogenase-related, conserved site / 3-hydroxyisobutyrate dehydrogenase signature. / 3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain / NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 ...3-hydroxyisobutyrate dehydrogenase-related, conserved site / 3-hydroxyisobutyrate dehydrogenase signature. / 3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain / NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NAD-dependent L-serine dehydrogenase
Similarity search - Component
Biological speciesPyrobaculum calidifontis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsYoneda, K. / Sakuraba, H. / Ohshima, T.
CitationJournal: Extremophiles / Year: 2018
Title: Crystal structure of the NADP+and tartrate-bound complex of L-serine 3-dehydrogenase from the hyperthermophilic archaeon Pyrobaculum calidifontis.
Authors: Yoneda, K. / Sakuraba, H. / Araki, T. / Ohshima, T.
History
DepositionFeb 27, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1May 15, 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _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

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Assembly

Deposited unit
A: 6-phosphogluconate dehydrogenase, NAD-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5792
Polymers32,8351
Non-polymers7431
Water3,567198
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 6-phosphogluconate dehydrogenase, NAD-binding protein
hetero molecules

A: 6-phosphogluconate dehydrogenase, NAD-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1574
Polymers65,6712
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area7640 Å2
ΔGint-49 kcal/mol
Surface area22590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.996, 57.348, 56.393
Angle α, β, γ (deg.)90.00, 106.73, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-506-

HOH

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Components

#1: Protein 6-phosphogluconate dehydrogenase, NAD-binding protein


Mass: 32835.266 Da / Num. of mol.: 1 / Mutation: K170M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum calidifontis (archaea) / Strain: JCM 11548 / VA1 / Gene: Pcal_0699 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: A3MU08, EC: 1.1.1.276
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.85 Å3/Da / Density % sol: 56.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 2.0M AMMONIUM SULFATE, 0.1M ACETATE BUFFER, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: PILATUS 2M-F / Detector: CCD / Date: Oct 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.44→57.938 Å / Num. obs: 67330 / Biso Wilson estimate: 16.4 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W6U

3w6u


Resolution: 1.44→46.8 Å /
RfactorNum. reflection
Rfree0.185 -
Rwork0.172 -
obs-64762
Refinement stepCycle: LAST / Resolution: 1.44→46.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2228 0 48 198 2474

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