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- PDB-4rf4: Crystal structure of ketoreductase from Lactobacillus kefir -

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Basic information

Entry
Database: PDB / ID: 4rf4
TitleCrystal structure of ketoreductase from Lactobacillus kefir
ComponentsNADPH dependent R-specific alcohol dehydrogenase
KeywordsOXIDOREDUCTASE
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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP-dependent (R)-specific alcohol dehydrogenase
Similarity search - Component
Biological speciesLactobacillus kefiri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.201 Å
AuthorsTang, Y. / Tibrewal, N. / Cascio, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Origins of stereoselectivity in evolved ketoreductases.
Authors: Noey, E.L. / Tibrewal, N. / Jimenez-Oses, G. / Osuna, S. / Park, J. / Bond, C.M. / Cascio, D. / Liang, J. / Zhang, X. / Huisman, G.W. / Tang, Y. / Houk, K.N.
History
DepositionSep 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2Dec 23, 2015Group: Database references
Revision 1.3Jan 6, 2016Group: Database references
Revision 1.4Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: NADPH dependent R-specific alcohol dehydrogenase
B: NADPH dependent R-specific alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0104
Polymers57,9612
Non-polymers492
Water64936
1
A: NADPH dependent R-specific alcohol dehydrogenase
B: NADPH dependent R-specific alcohol dehydrogenase
hetero molecules

A: NADPH dependent R-specific alcohol dehydrogenase
B: NADPH dependent R-specific alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,0208
Polymers115,9234
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area14150 Å2
ΔGint-112 kcal/mol
Surface area29970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.170, 71.670, 67.580
Angle α, β, γ (deg.)90.000, 106.560, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-301-

MG

21B-301-

MG

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLN / End label comp-ID: GLN / Auth seq-ID: 3 - 252 / Label seq-ID: 23 - 272

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein NADPH dependent R-specific alcohol dehydrogenase / Ketoreductase


Mass: 28980.658 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus kefiri (bacteria) / Gene: adhR / Plasmid: pHis8 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6WVP7
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.15 Å3/Da / Density % sol: 42.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M magnesium formate, 15% w/v PEG3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 11, 2013
RadiationMonochromator: Cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→64.777 Å / Num. obs: 24812 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.07 Å2 / Rmerge(I) obs: 0.123 / Χ2: 0.953 / Net I/σ(I): 14.94
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.2-2.260.464.93121301818198.8
2.26-2.320.3836123881785199.4
2.32-2.390.3317.19121001732198.9
2.39-2.460.3077.65117861687199.7
2.46-2.540.2817.99111051613199.9
2.54-2.630.2359.28107751580199.2
2.63-2.730.2159.9102441544199.3
2.73-2.840.17610.7188781436197.4
2.84-2.970.15613.421019814191100
2.97-3.110.12515.8396101342199.7
3.11-3.280.10917.7591351285199.4
3.28-3.480.09320.8885061213199.7
3.48-3.720.07424.4579751166199.7
3.72-4.020.06426.4967811061198.2
4.02-4.40.05429.066252946197.7
4.4-4.920.05332.156518912199.7
4.92-5.680.06227.485505789199.7
5.68-6.960.06824.234554674199.7
6.96-9.840.04433.823127508195.5
9.84-64.80.04134.471997302199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.2 Å64.78 Å
Translation2.2 Å64.78 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.5phasing
PHENIXdev_1555refinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NXQ

1nxq


Resolution: 2.201→64.777 Å / FOM work R set: 0.7605 / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2948 2481 10 %RANDOM
Rwork0.2351 ---
obs0.2411 24800 99.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.41 Å2 / Biso mean: 21.08 Å2 / Biso min: 9.13 Å2
Refinement stepCycle: LAST / Resolution: 2.201→64.777 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3657 0 2 36 3695
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083715
X-RAY DIFFRACTIONf_angle_d0.9965040
X-RAY DIFFRACTIONf_chiral_restr0.034591
X-RAY DIFFRACTIONf_plane_restr0.004654
X-RAY DIFFRACTIONf_dihedral_angle_d11.6461298
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2220X-RAY DIFFRACTION0.612TORSIONAL
12B2220X-RAY DIFFRACTION0.612TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.201-2.24340.43231360.29411218135498
2.2434-2.28920.35481390.25791248138799
2.2892-2.3390.32881360.22941224136099
2.339-2.39340.2911380.22691248138699
2.3934-2.45330.30931360.238112241360100
2.4533-2.51960.30051360.2361222135899
2.5196-2.59370.31731410.23381265140699
2.5937-2.67750.32251360.2231229136599
2.6775-2.77320.2851350.23191206134199
2.7732-2.88420.25861370.21761242137998
2.8842-3.01550.24731390.227712431382100
3.0155-3.17440.31871370.235712411378100
3.1744-3.37330.26751390.225612521391100
3.3733-3.63370.30711380.22681246138499
3.6337-3.99940.27781380.22111243138199
3.9994-4.5780.29311380.23051236137498
4.578-5.76720.2781400.24812591399100
5.7672-64.80460.27181420.25811273141598
Refinement TLS params.Method: refined / Origin x: 103.07 Å / Origin y: -1.2312 Å / Origin z: 66.551 Å
111213212223313233
T0.1165 Å2-0.0057 Å20.0068 Å2-0.125 Å2-0.0032 Å2--0.1284 Å2
L0.4265 °20.0569 °2-0.2037 °2-0.2492 °2-0.0108 °2--0.9231 °2
S-0.0108 Å °-0.0344 Å °-0.0077 Å °0.0109 Å °-0.0058 Å °-0.0473 Å °-0.0265 Å °0.1276 Å °0.0158 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 416
2X-RAY DIFFRACTION1allB3 - 420

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