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- PDB-5x8h: Crystal structure of the ketone reductase ChKRED20 from the genom... -

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Basic information

Entry
Database: PDB / ID: 5x8h
TitleCrystal structure of the ketone reductase ChKRED20 from the genome of Chryseobacterium sp. CA49
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
Short-chain dehydrogenase reductase
Similarity search - Component
Biological speciesChryseobacterium sp. CA49 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsZhao, F.J. / Jin, Y. / Liu, Z.C. / Wang, G.G. / Wu, Z.L.
CitationJournal: Appl. Microbiol. Biotechnol. / Year: 2017
Title: Crystal structure and iterative saturation mutagenesis of ChKRED20 for expanded catalytic scope
Authors: Zhao, F.J. / Jin, Y. / Liu, Z. / Guo, C. / Li, T.B. / Li, Z.Y. / Wang, G. / Wu, Z.L.
History
DepositionMar 2, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Nov 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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


Theoretical massNumber of molelcules
Total (without water)105,0354
Polymers105,0354
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12490 Å2
ΔGint-96 kcal/mol
Surface area34250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.826, 102.867, 109.380
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 / Ketone reductase ChKRED 20


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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.33 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M NaCl, 0.1M HEPES, 1.6M (NH4)2SO4, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9754 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9754 Å / Relative weight: 1
ReflectionResolution: 1.85→29.7 Å / Num. obs: 83764 / % possible obs: 99.3 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.1
Reflection shellResolution: 1.85→1.88 Å / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 4082 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NI5

4ni5


Resolution: 1.85→29.7 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.577 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22993 4080 4.9 %RANDOM
Rwork0.19451 ---
obs0.1963 79619 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.306 Å2
Baniso -1Baniso -2Baniso -3
1--2.98 Å2-0 Å20 Å2
2--3.24 Å20 Å2
3----0.26 Å2
Refinement stepCycle: 1 / Resolution: 1.85→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7332 0 0 131 7463
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0197440
X-RAY DIFFRACTIONr_bond_other_d0.0020.027196
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.97310048
X-RAY DIFFRACTIONr_angle_other_deg0.991316612
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3765988
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.75625.753292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.332151280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9191520
X-RAY DIFFRACTIONr_chiral_restr0.1010.21140
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028560
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021532
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_it2.7893.813964
X-RAY DIFFRACTIONr_mcbond_other2.7893.813963
X-RAY DIFFRACTIONr_mcangle_it3.5635.74948
X-RAY DIFFRACTIONr_mcangle_other3.5635.74949
X-RAY DIFFRACTIONr_scbond_it3.464.223476
X-RAY DIFFRACTIONr_scbond_other3.464.223476
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0046.1535100
X-RAY DIFFRACTIONr_long_range_B_refined5.95630.0228258
X-RAY DIFFRACTIONr_long_range_B_other5.94529.9858210
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.848→1.896 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 301 -
Rwork0.273 5694 -
obs--97.18 %

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