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- PDB-6ixm: Crystal structure of the ketone reductase ChKRED20 from the genom... -

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Basic information

Entry
Database: PDB / ID: 6ixm
TitleCrystal structure of the ketone reductase ChKRED20 from the genome of Chryseobacterium sp. CA49 complexed with NAD
ComponentsShort-chain dehydrogenase reductase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


oxidoreductase activity / nucleotide 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Short-chain dehydrogenase reductase
Similarity search - Component
Biological speciesChryseobacterium sp. CA49 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 Å
AuthorsZhao, F.J. / Jin, Y. / Liu, Z.C. / Wang, G.G. / Wu, Z.L.
CitationJournal: Enzyme Microb. Technol. / Year: 2019
Title: Structure-guided engineering of ChKRED20 from Chryseobacterium sp. CA49 for asymmetric reduction of aryl ketoesters.
Authors: Li, T.B. / Zhao, F.J. / Liu, Z. / Jin, Y. / Liu, Y. / Pei, X.Q. / Zhang, Z.G. / Wang, G. / Wu, Z.L.
History
DepositionDec 11, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2019Provider: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Short-chain dehydrogenase reductase
B: Short-chain dehydrogenase reductase
C: Short-chain dehydrogenase reductase
D: Short-chain dehydrogenase reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,0257
Polymers105,0354
Non-polymers1,9903
Water20,4831137
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15800 Å2
ΔGint-114 kcal/mol
Surface area32610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.891, 113.980, 131.819
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Short-chain dehydrogenase reductase


Mass: 26258.797 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chryseobacterium sp. CA49 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: X2D0L0
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1137 / 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: 2.28 Å3/Da / Density % sol: 46.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M NaCl, 0.1M HEPES, 1.6M (NH4)SO4, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9754 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9754 Å / Relative weight: 1
ReflectionResolution: 1.6→29.3 Å / Num. obs: 126974 / % possible obs: 99.9 % / Redundancy: 6.7 % / Net I/σ(I): 21.7
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 4.4 / Num. unique obs: 6312 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NI5

4ni5


Resolution: 1.601→29.288 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.44
RfactorNum. reflection% reflection
Rfree0.1917 6266 4.94 %
Rwork0.1637 --
obs0.1651 126717 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.601→29.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7254 0 132 1137 8523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067504
X-RAY DIFFRACTIONf_angle_d0.82310156
X-RAY DIFFRACTIONf_dihedral_angle_d4.3034494
X-RAY DIFFRACTIONf_chiral_restr0.0581155
X-RAY DIFFRACTIONf_plane_restr0.0051309
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6007-1.61890.26222100.1993647X-RAY DIFFRACTION93
1.6189-1.63790.21732100.19053990X-RAY DIFFRACTION99
1.6379-1.65790.21562030.18213945X-RAY DIFFRACTION100
1.6579-1.67890.18282160.17813991X-RAY DIFFRACTION100
1.6789-1.7010.22172070.17113979X-RAY DIFFRACTION100
1.701-1.72430.20292130.174000X-RAY DIFFRACTION100
1.7243-1.74890.21091940.17063974X-RAY DIFFRACTION100
1.7489-1.7750.2062060.1674000X-RAY DIFFRACTION100
1.775-1.80270.18931940.1643991X-RAY DIFFRACTION100
1.8027-1.83230.20982110.16734014X-RAY DIFFRACTION100
1.8323-1.86390.21052130.16883969X-RAY DIFFRACTION100
1.8639-1.89780.23062040.17564001X-RAY DIFFRACTION100
1.8978-1.93430.18622490.17233975X-RAY DIFFRACTION100
1.9343-1.97370.2132180.16383973X-RAY DIFFRACTION100
1.9737-2.01660.18681850.16164014X-RAY DIFFRACTION100
2.0166-2.06350.21492020.16584046X-RAY DIFFRACTION100
2.0635-2.11510.19432130.16143991X-RAY DIFFRACTION100
2.1151-2.17230.21022290.15743980X-RAY DIFFRACTION100
2.1723-2.23620.20171820.15944054X-RAY DIFFRACTION100
2.2362-2.30830.16442050.15533988X-RAY DIFFRACTION100
2.3083-2.39080.18041990.15564039X-RAY DIFFRACTION100
2.3908-2.48650.2022200.15844047X-RAY DIFFRACTION100
2.4865-2.59960.20111990.16134036X-RAY DIFFRACTION100
2.5996-2.73650.18912010.16864056X-RAY DIFFRACTION100
2.7365-2.90790.20022230.1634060X-RAY DIFFRACTION100
2.9079-3.13210.19162060.16684040X-RAY DIFFRACTION100
3.1321-3.44690.19412180.16254070X-RAY DIFFRACTION100
3.4469-3.94460.17331930.15174129X-RAY DIFFRACTION100
3.9446-4.96590.14952150.1464146X-RAY DIFFRACTION100
4.9659-29.29310.1822280.17834306X-RAY DIFFRACTION100

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