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- PDB-5wva: Serratia marcescens short-chain dehydrogenase/reductase F98Y/F202... -

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Basic information

Entry
Database: PDB / ID: 5wva
TitleSerratia marcescens short-chain dehydrogenase/reductase F98Y/F202Y mutant
ComponentsShort-chain dehydrogenase
KeywordsOXIDOREDUCTASE / Serratia marcescens / short-chain dehydrogenase/reductase / F98Y/F202Y mutant
Function / homologyEnoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / nucleotide binding / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Short-chain dehydrogenase
Function and homology information
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsLiu, J.S. / Tsou, Y. / Wang, W.C.
CitationJournal: Sci Rep / Year: 2018
Title: Structure-guided design of Serratia marcescens short-chain dehydrogenase/reductase for stereoselective synthesis of (R)-phenylephrine.
Authors: Liu, J.-S. / Kuan, Y.-C. / Tsou, Y. / Lin, T.-Y. / Hsu, W.-H. / Yang, M.-T. / Lin, J.-Y. / Wang, W.-C.
History
DepositionDec 23, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Short-chain dehydrogenase
B: Short-chain dehydrogenase


Theoretical massNumber of molelcules
Total (without water)59,3712
Polymers59,3712
Non-polymers00
Water6,215345
1
A: Short-chain dehydrogenase
B: Short-chain dehydrogenase

A: Short-chain dehydrogenase
B: Short-chain dehydrogenase


Theoretical massNumber of molelcules
Total (without water)118,7414
Polymers118,7414
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area13090 Å2
ΔGint-62 kcal/mol
Surface area29290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.925, 83.925, 115.038
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Short-chain dehydrogenase


Mass: 29685.363 Da / Num. of mol.: 2 / Mutation: F98Y, F202Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A192ICX3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 1.71 Å3/Da / Density % sol: 27.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50mM HEPES buffer (pH 7.0), 40% (v/v) tacsimate (pH 7.0), 2mM spermine, 2mM hexamine cobalt (III) chloride

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.47→67.55 Å / Num. obs: 70468 / % possible obs: 100 % / Redundancy: 28.1 % / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.009 / Net I/σ(I): 85.1
Reflection shellResolution: 1.47→1.52 Å / CC1/2: 0.999

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZGW

4zgw


Resolution: 1.47→67.55 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.07 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20663 3391 4.9 %RANDOM
Rwork0.17483 ---
obs0.17638 66030 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.083 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.2 Å2
Refinement stepCycle: 1 / Resolution: 1.47→67.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3321 0 0 347 3668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0193365
X-RAY DIFFRACTIONr_bond_other_d0.0020.023274
X-RAY DIFFRACTIONr_angle_refined_deg2.541.9554553
X-RAY DIFFRACTIONr_angle_other_deg1.23537473
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7335459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91323.955134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55815517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4431523
X-RAY DIFFRACTIONr_chiral_restr0.1550.2525
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023965
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02762
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_it1.8591.411848
X-RAY DIFFRACTIONr_mcbond_other1.8591.411847
X-RAY DIFFRACTIONr_mcangle_it2.6272.1122303
X-RAY DIFFRACTIONr_mcangle_other2.6262.1122304
X-RAY DIFFRACTIONr_scbond_it3.3341.7921517
X-RAY DIFFRACTIONr_scbond_other3.3331.7921518
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8362.5572251
X-RAY DIFFRACTIONr_long_range_B_refined5.61914.81614975
X-RAY DIFFRACTIONr_long_range_B_other5.44114.23914483
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.47→1.508 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 243 -
Rwork0.187 4869 -
obs--99.86 %

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