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- PDB-9fe6: Short-chain dehydrogenase/reductase (SDR) from Thermus caliditerrae -

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Basic information

Entry
Database: PDB / ID: 9fe6
TitleShort-chain dehydrogenase/reductase (SDR) from Thermus caliditerrae
ComponentsSDR family oxidoreductase
KeywordsOXIDOREDUCTASE / short chain dehydrogenase / ketoreductase / biocatalysis
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
: / PKS_KR / 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
SDR family oxidoreductase
Similarity search - Component
Biological speciesThermus caliditerrae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.875 Å
AuthorsKapur, B. / Nar, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Front Chem Biol / Year: 2024
Title: In silico enzyme screening identifies an SDR ketoreductase from Thermus caliditerrae as an attractive biocatalyst and promising candidate for protein engineering
Authors: Sosa, Y. / Kapur, B. / Hurtak, J. / Kingsley, L. / Wu, H. / Gruber, S. / Nar, H. / Khattabi, S. / Moral, J. / Lucas, M. / Martin, C. / Loncar, N. / Buono, F. / Pefaur, N. / Nixon, A.E. / Song, J.
History
DepositionMay 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SDR family oxidoreductase
B: SDR family oxidoreductase
C: SDR family oxidoreductase
D: SDR family oxidoreductase
E: SDR family oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,9827
Polymers150,9345
Non-polymers492
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14810 Å2
ΔGint-110 kcal/mol
Surface area38390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.673, 122.989, 163.347
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
SDR family oxidoreductase


Mass: 30186.771 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: Additional electron density is present for the linker peptide LVPR in the structure. This peptide represents the thrombin cleavage site and are visible near the N-termini of Chain A and ...Details: Additional electron density is present for the linker peptide LVPR in the structure. This peptide represents the thrombin cleavage site and are visible near the N-termini of Chain A and Chain D and is referred to as Chain E. The assignment of this chain was not performed due to the ambiguity regarding which chain it belongs to.
Source: (gene. exp.) Thermus caliditerrae (bacteria) / Gene: ENM28_03685 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7C5VFX3
#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


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.89 Å3/Da / Density % sol: 34.78 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris, 0.3M magnesium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.000053 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000053 Å / Relative weight: 1
ReflectionResolution: 1.875→98.253 Å / Num. obs: 49723 / % possible obs: 93 % / Redundancy: 13.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.039 / Net I/σ(I): 10.6
Reflection shellResolution: 1.875→2.162 Å / Redundancy: 14.4 % / Rmerge(I) obs: 1.489 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2486 / CC1/2: 0.722 / Rpim(I) all: 0.405

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.875→98.25 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.906 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.352 / SU Rfree Blow DPI: 0.228
RfactorNum. reflection% reflectionSelection details
Rfree0.2446 2522 -RANDOM
Rwork0.2174 ---
obs0.2187 49723 52.6 %-
Displacement parametersBiso mean: 53.86 Å2
Baniso -1Baniso -2Baniso -3
1--8.0933 Å20 Å20 Å2
2--0.0082 Å20 Å2
3---8.0851 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 1.875→98.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7921 0 2 282 8205
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00816191HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9429363HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4927SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2594HARMONIC5
X-RAY DIFFRACTIONt_it16191HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1052SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact13652SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion14.15
LS refinement shellResolution: 1.88→2.05 Å
RfactorNum. reflection% reflection
Rfree0.3151 38 -
Rwork0.2766 --
obs0.2781 995 4.56 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3647-0.0342-0.1661.0698-0.11320.7483-0.22310.02350.04340.02350.03220.1930.04340.1930.1909-0.21880.07950.12490.01910.27460.4345-6.5517-9.396-17.1684
22.0007-0.2141-0.12731.3268-0.1080.2575-0.1089-0.2002-0.0038-0.20020.0478-0.0912-0.0038-0.09120.0611-0.0946-0.08210.04970.0257-0.18620.1528-21.4261-0.1211-44.8358
33.1221-0.0361-0.08451.22390.06680.9988-0.0555-0.0623-0.1576-0.06230.02290.0193-0.15760.01930.0326-0.1041-0.0245-0.0266-0.08790.00470.225-12.024928.9959-36.6331
40.5495-0.0935-0.46592.0023-0.25311.5041-0.05440.2918-0.25240.2918-0.04190.1466-0.25240.14660.0964-0.11780.00330.00540.2109-0.03880.0116-14.86619.3185-6.7662
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 261
2X-RAY DIFFRACTION2{ B|* }B1 - 261
3X-RAY DIFFRACTION3{ C|* }C1 - 261
4X-RAY DIFFRACTION4{ D|* }D1 - 261

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