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- PDB-5gwt: 4-hydroxyisoleucine dehydrogenase mutant complexed with NADH and ... -

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Basic information

Entry
Database: PDB / ID: 5gwt
Title4-hydroxyisoleucine dehydrogenase mutant complexed with NADH and succinate
Components4-hydroxyisolecuine dehydrogenase
KeywordsOXIDOREDUCTASE / NADH-dependent / short-chain / dehydrogenase / reductase
Function / homology
Function and homology information


Oxidoreductases / oxidoreductase activity
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / SUCCINIC ACID / 3-oxoacyl-ACP reductase
Similarity search - Component
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsShi, X. / Miyakawa, T. / Nakamura, A. / Tanokura, M.
CitationJournal: Sci Rep / Year: 2017
Title: Engineering a short-chain dehydrogenase/reductase for the stereoselective production of (2S,3R,4S)-4-hydroxyisoleucine with three asymmetric centers.
Authors: Shi, X. / Miyakawa, T. / Nakamura, A. / Hou, F. / Hibi, M. / Ogawa, J. / Kwon, Y. / Tanokura, M.
History
DepositionSep 13, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: 4-hydroxyisolecuine dehydrogenase
B: 4-hydroxyisolecuine dehydrogenase
C: 4-hydroxyisolecuine dehydrogenase
D: 4-hydroxyisolecuine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,31312
Polymers123,1874
Non-polymers3,1268
Water6,900383
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20640 Å2
ΔGint-111 kcal/mol
Surface area33300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)231.846, 231.846, 78.957
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
4-hydroxyisolecuine dehydrogenase


Mass: 30796.660 Da / Num. of mol.: 4 / Mutation: E144K, w242q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Strain: 2e2 / Gene: AC241_05390 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0K0Q8K4
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 3.24 Å3/Da / Density % sol: 62.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.8 M succinate, pH 7.0

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: CCD / Date: Oct 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→45.5 Å / Num. obs: 124974 / % possible obs: 99.7 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 16
Reflection shellResolution: 1.9→2.01 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F9I

3f9i


Resolution: 1.9→45.5 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.547 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.098 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20058 2100 1.7 %RANDOM
Rwork0.17449 ---
obs0.17493 122874 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.248 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0.06 Å20 Å2
2---0.12 Å20 Å2
3---0.39 Å2
Refinement stepCycle: 1 / Resolution: 1.9→45.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7716 0 16 383 8115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0197860
X-RAY DIFFRACTIONr_bond_other_d0.0020.027720
X-RAY DIFFRACTIONr_angle_refined_deg2.2251.99610636
X-RAY DIFFRACTIONr_angle_other_deg1.169317792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2465968
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.45125.455308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.392151444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0211528
X-RAY DIFFRACTIONr_chiral_restr0.1560.21248
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.028672
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021688
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6352.223884
X-RAY DIFFRACTIONr_mcbond_other2.6352.223883
X-RAY DIFFRACTIONr_mcangle_it3.5453.314848
X-RAY DIFFRACTIONr_mcangle_other3.5443.3114849
X-RAY DIFFRACTIONr_scbond_it4.0852.7033976
X-RAY DIFFRACTIONr_scbond_other4.0852.7043977
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9663.8485789
X-RAY DIFFRACTIONr_long_range_B_refined7.26618.5549080
X-RAY DIFFRACTIONr_long_range_B_other7.23718.4518959
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.897→1.946 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.597 151 -
Rwork0.526 8854 -
obs--97.16 %

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