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- PDB-8kcn: X-ray structure of 3-alpha-(Or 20-beta)-hydroxysteroid dehydrogen... -

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Basic information

Entry
Database: PDB / ID: 8kcn
TitleX-ray structure of 3-alpha-(Or 20-beta)-hydroxysteroid dehydrogenase mutant
ComponentsNADP-dependent (R)-specific alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / 3-alpha-(Or 20-beta)-hydroxysteroid dehydrogenase
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity / nucleotide binding / metal ion binding
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
NADP-dependent (R)-specific alcohol dehydrogenase
Similarity search - Component
Biological speciesLactobacillaceae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsSong, S.K. / Ma, Q.Q. / Lv, D.Q. / Cheng, C.Y. / Su, Z.D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: to be published
Title: X-ray structure of 3-alpha-(Or 20-beta)-hydroxysteroid dehydrogenase mutant
Authors: Song, S.K. / Ma, Q.Q. / Lv, D.Q. / Cheng, X.Y. / Su, Z.D.
History
DepositionAug 8, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADP-dependent (R)-specific alcohol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)26,6801
Polymers26,6801
Non-polymers00
Water3,135174
1
A: NADP-dependent (R)-specific alcohol dehydrogenase

A: NADP-dependent (R)-specific alcohol dehydrogenase

A: NADP-dependent (R)-specific alcohol dehydrogenase

A: NADP-dependent (R)-specific alcohol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)106,7214
Polymers106,7214
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area13500 Å2
ΔGint-71 kcal/mol
Surface area32670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.527, 79.617, 114.488
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-399-

HOH

21A-469-

HOH

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Components

#1: Protein NADP-dependent (R)-specific alcohol dehydrogenase


Mass: 26680.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillaceae (bacteria) / Gene: adh / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q6WVP7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 30% PEG MME550; 0.1M Tris pH7.0; 0.05M MgCL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 1, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.31→65.365 Å / Num. obs: 60439 / % possible obs: 98.9 % / Redundancy: 1.9 % / CC1/2: 0.996 / Net I/σ(I): 14.9
Reflection shellResolution: 1.31→1.31 Å / Rmerge(I) obs: 0.1624 / Num. unique obs: 57490 / Rrim(I) all: 0.1792 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
HKL-3000data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.31→31.47 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.586 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1729 2947 4.9 %RANDOM
Rwork0.16236 ---
obs0.16287 57490 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0 Å2-0 Å2
2--0.55 Å2-0 Å2
3----0.27 Å2
Refinement stepCycle: 1 / Resolution: 1.31→31.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1862 0 0 174 2036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0121891
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161813
X-RAY DIFFRACTIONr_angle_refined_deg1.8131.6432558
X-RAY DIFFRACTIONr_angle_other_deg0.5751.5774179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4295249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.73859
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.44910321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0920.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022231
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02403
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_it0.7920.689999
X-RAY DIFFRACTIONr_mcbond_other0.7910.689999
X-RAY DIFFRACTIONr_mcangle_it1.1631.2391247
X-RAY DIFFRACTIONr_mcangle_other1.1621.2391248
X-RAY DIFFRACTIONr_scbond_it2.4070.949892
X-RAY DIFFRACTIONr_scbond_other2.4050.949893
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5721.611312
X-RAY DIFFRACTIONr_long_range_B_refined4.0888.272114
X-RAY DIFFRACTIONr_long_range_B_other4.0368.022083
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.31→1.344 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 196 -
Rwork0.199 3722 -
obs--87.89 %

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