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- PDB-4rf3: Crystal Structure of ketoreductase from Lactobacillus kefir, muta... -

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Basic information

Entry
Database: PDB / ID: 4rf3
TitleCrystal Structure of ketoreductase from Lactobacillus kefir, mutant A94F
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, acting on the CH-OH group of donors, NAD or NADP as acceptor / 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: 1.694 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_atom_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_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_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)58,4387
Polymers58,1142
Non-polymers3255
Water2,468137
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)116,87714
Polymers116,2274
Non-polymers65010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area14670 Å2
ΔGint-102 kcal/mol
Surface area30680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.150, 110.670, 67.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: GLN / End label comp-ID: GLN

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1THRTHRchain AAA2 - 25222 - 272
2ASPASPchain BBB3 - 25223 - 272

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Components

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


Mass: 29056.756 Da / Num. of mol.: 2 / Mutation: A94F
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.13 Å3/Da / Density % sol: 42.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.6 M magnesium chloride, 0.1 M Bis-Tris, pH 5.5, 20% w/v PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 9, 2013
RadiationMonochromator: Cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.69→67.61 Å / Num. obs: 46947 / % possible obs: 84 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.45 Å2 / Rmerge(I) obs: 0.101 / Χ2: 0.955 / Net I/σ(I): 9.54
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.69-1.740.4712.2798803288181.2
1.74-1.790.4122.85112883503187.6
1.79-1.840.3333.45102603265184.5
1.84-1.890.2674.26109913360189.3
1.89-1.960.235.21105733226188.6
1.96-2.020.196.19100543100188.1
2.02-2.10.1627.0994912960186.2
2.1-2.190.1378.4884102609179.3
2.19-2.280.1369.5190952729186.3
2.28-2.40.11910.5988562597185.5
2.4-2.530.11411.1583572445185.2
2.53-2.680.11812.5679082288183.8
2.68-2.860.08613.6967502004177
2.86-3.090.09715.9972732002183.5
3.09-3.390.07917.8967421867183.3
3.39-3.790.0719.7357501647181.7
3.79-4.370.06222.1147891370176.1
4.37-5.360.05623.0345401234179.9
5.36-7.580.05720.493327938177
7.58-67.610.04325.021822515171.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.11 Å66.15 Å
Translation5.11 Å66.15 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: 1.694→56.78 Å / FOM work R set: 0.8066 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2415 4693 10 %RANDOM
Rwork0.2077 ---
obs0.2112 46936 83.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.85 Å2 / Biso mean: 19.36 Å2 / Biso min: 9.63 Å2
Refinement stepCycle: LAST / Resolution: 1.694→56.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3691 0 20 137 3848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073766
X-RAY DIFFRACTIONf_angle_d0.9855099
X-RAY DIFFRACTIONf_chiral_restr0.041593
X-RAY DIFFRACTIONf_plane_restr0.005658
X-RAY DIFFRACTIONf_dihedral_angle_d10.9321324
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2228X-RAY DIFFRACTION2.693TORSIONAL
12B2228X-RAY DIFFRACTION2.693TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.694-1.71330.35681290.35661162129171
1.7133-1.73340.32561640.25991480164489
1.7334-1.75460.30641640.25721482164689
1.7546-1.77680.31611590.25951429158887
1.7768-1.80020.34261530.24791372152584
1.8002-1.82480.29691530.25071385153883
1.8248-1.85090.29431670.23251498166590
1.8509-1.87850.26031650.2321481164689
1.8785-1.90790.26671620.22231463162589
1.9079-1.93920.30111640.21931479164388
1.9392-1.97260.26231620.2251456161889
1.9726-2.00850.27091650.22271481164688
2.0085-2.04710.28031590.20821433159287
2.0471-2.08890.24821590.22291424158386
2.0889-2.13430.28031540.22161390154484
2.1343-2.1840.26631430.22191287143076
2.184-2.23860.26341590.22131432159186
2.2386-2.29910.24331600.21121439159987
2.2991-2.36680.24851590.21851425158485
2.3668-2.44320.31241580.22771431158985
2.4432-2.53050.24111570.23321416157385
2.5305-2.63180.25761580.21491422158084
2.6318-2.75160.21681500.22071348149880
2.7516-2.89660.27511430.2371290143377
2.8966-3.07810.24261600.20741440160084
3.0781-3.31570.21921560.19121405156184
3.3157-3.64940.18931570.17741407156482
3.6494-4.17730.17931450.161305145076
4.1773-5.26240.17491550.1521398155380
5.2624-56.8120.20071540.18611383153775
Refinement TLS params.Method: refined / Origin x: -4.563 Å / Origin y: 14.686 Å / Origin z: 11.213 Å
111213212223313233
T0.1563 Å20.0044 Å2-0.0026 Å2-0.142 Å2-0.0023 Å2--0.0873 Å2
L0.1626 °2-0.0486 °2-0.0332 °2-0.236 °2-0.0834 °2--0.4482 °2
S-0.0098 Å °-0.0387 Å °0.0073 Å °0.047 Å °0.0009 Å °0.0111 Å °-0.0471 Å °-0.0159 Å °0.0061 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:252 OR RESID 301:301 OR RESID 401:537 OR RESID 302:302 ) ) OR ( CHAIN B AND ( RESID 3:252 OR RESID 301:303 ) )A2 - 252
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:252 OR RESID 301:301 OR RESID 401:537 OR RESID 302:302 ) ) OR ( CHAIN B AND ( RESID 3:252 OR RESID 301:303 ) )A301
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:252 OR RESID 301:301 OR RESID 401:537 OR RESID 302:302 ) ) OR ( CHAIN B AND ( RESID 3:252 OR RESID 301:303 ) )A401 - 537
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:252 OR RESID 301:301 OR RESID 401:537 OR RESID 302:302 ) ) OR ( CHAIN B AND ( RESID 3:252 OR RESID 301:303 ) )A302
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:252 OR RESID 301:301 OR RESID 401:537 OR RESID 302:302 ) ) OR ( CHAIN B AND ( RESID 3:252 OR RESID 301:303 ) )B3 - 252
6X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:252 OR RESID 301:301 OR RESID 401:537 OR RESID 302:302 ) ) OR ( CHAIN B AND ( RESID 3:252 OR RESID 301:303 ) )B301 - 303

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