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- PDB-7yic: Crystal structure of reductase LSADH -

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Basic information

Entry
Database: PDB / ID: 7yic
TitleCrystal structure of reductase LSADH
ComponentsShort chain alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / short chain alcohol dehydrogenase
Function / homology: / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / oxidoreductase activity / NAD(P)-binding domain superfamily / Short chain alcohol dehydrogenase
Function and homology information
Biological speciesLeifsonia sp. S749 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsTang, J. / Liuqing, C.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: crystal structure of reductase LSADH
Authors: Tang, J. / Liuqing, C.
History
DepositionJul 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,7722
Polymers49,7722
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-18 kcal/mol
Surface area18980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.280, 109.928, 120.668
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Short chain alcohol dehydrogenase


Mass: 24885.854 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leifsonia sp. S749 (bacteria) / Gene: lsadh
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q4R1E0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.31 Å3/Da / Density % sol: 46.71 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: peg 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Feb 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.16→20 Å / Num. obs: 24544 / % possible obs: 97.65 % / Redundancy: 2 % / CC1/2: 0.75 / Net I/σ(I): 2.3
Reflection shellResolution: 2.16→2.34 Å / Num. unique obs: 10327 / CC1/2: 0.75

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H5X

5h5x


Resolution: 2.16→19.81 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.896 / SU B: 65.012 / SU ML: 0.558 / Cross valid method: THROUGHOUT / ESU R: 0.403 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.324 1213 4.9 %RANDOM
Rwork0.296 ---
obs0.297 23331 97.9 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.62 Å2
Baniso -1Baniso -2Baniso -3
1--9.78 Å20 Å20 Å2
2--5.53 Å20 Å2
3---4.25 Å2
Refinement stepCycle: LAST / Resolution: 2.16→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3504 0 0 14 3518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0183554
X-RAY DIFFRACTIONr_bond_other_d0.0050.023402
X-RAY DIFFRACTIONr_angle_refined_deg1.2951.8694844
X-RAY DIFFRACTIONr_angle_other_deg1.0492.7837774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9135498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80324.028144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.16215498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6181512
X-RAY DIFFRACTIONr_chiral_restr0.0690.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024232
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02768
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_it0.0730.9491998
X-RAY DIFFRACTIONr_mcbond_other0.0730.9491997
X-RAY DIFFRACTIONr_mcangle_it0.1391.4232494
X-RAY DIFFRACTIONr_mcangle_other0.1391.4232495
X-RAY DIFFRACTIONr_scbond_it0.0270.9581554
X-RAY DIFFRACTIONr_scbond_other0.0270.9581555
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.0661.4362351
X-RAY DIFFRACTIONr_long_range_B_refined1.08811.8444001
X-RAY DIFFRACTIONr_long_range_B_other1.08411.8284001
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.16→2.22 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.477 77 -
Rwork0.504 1294 -
obs--75.91 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.19980.0458-0.33051.7429-0.12831.61530.01680.04510.0251-0.0110.01190.1541-0.0076-0.2009-0.02861.4870.0027-0.02170.03590.00390.016529.05347.19916.591
20.8121-0.33840.37011.6116-0.07711.33280.01090.1495-0.2035-0.1245-0.0431-0.11980.12070.02470.03221.54310.00070.03390.0298-0.04480.094835.21216.67815.518
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 251
2X-RAY DIFFRACTION2B2 - 251

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