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- PDB-7xqm: InDel-mutant short chain Dehydrogenase bound to SAH -

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Basic information

Entry
Database: PDB / ID: 7xqm
TitleInDel-mutant short chain Dehydrogenase bound to SAH
ComponentsDehydrogenase
KeywordsBIOSYNTHETIC PROTEIN / Rossmann / mutant / InDel design / coenzyme-switch
Function / homologyShort-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / oxidoreductase activity / NAD(P)-binding domain superfamily / S-ADENOSYL-L-HOMOCYSTEINE / Dehydrogenase
Function and homology information
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsToledo-Patino, S. / Laurino, P.
Funding support Japan, 1items
OrganizationGrant numberCountry
Other government Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Insertions and deletions mediated functional divergence of Rossmann fold enzymes.
Authors: Toledo-Patino, S. / Pascarelli, S. / Uechi, G.I. / Laurino, P.
History
DepositionMay 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dehydrogenase
B: Dehydrogenase
C: Dehydrogenase
D: Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,9608
Polymers106,4224
Non-polymers1,5384
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15280 Å2
ΔGint-122 kcal/mol
Surface area33860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.380, 82.760, 92.660
Angle α, β, γ (deg.)90.000, 111.995, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

#1: Protein
Dehydrogenase


Mass: 26605.602 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Strain: HB27 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72LQ6
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45.17 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 6% v/v 2-propanol, 0.1 M sodium acetate trihydrate pH 4.5 and 26% v/v polyethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→44.01 Å / Num. obs: 25837 / % possible obs: 98.6 % / Redundancy: 2.8 % / Biso Wilson estimate: 26.42 Å2 / CC1/2: 0.997 / Net I/σ(I): 24.05
Reflection shellResolution: 2.71→8.13 Å / Num. unique obs: 25801 / CC1/2: 0.996

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2d1y

2d1y


Resolution: 2.71→44.01 Å / SU ML: 0.1872 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 16.9728
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1815 1999 7.75 %RANDOM
Rwork0.1811 23792 --
obs0.1811 25791 98.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.16 Å2
Refinement stepCycle: LAST / Resolution: 2.71→44.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7432 0 104 124 7660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01397652
X-RAY DIFFRACTIONf_angle_d1.550910386
X-RAY DIFFRACTIONf_chiral_restr0.07841218
X-RAY DIFFRACTIONf_plane_restr0.00551364
X-RAY DIFFRACTIONf_dihedral_angle_d14.21882750
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-2.780.1941200.2071433X-RAY DIFFRACTION84.13
2.78-2.850.19931430.19891691X-RAY DIFFRACTION97.81
2.85-2.940.18771420.19151697X-RAY DIFFRACTION99.89
2.94-3.030.18651440.19221716X-RAY DIFFRACTION99.95
3.03-3.140.21281430.1981699X-RAY DIFFRACTION100
3.14-3.270.17661460.19061737X-RAY DIFFRACTION100
3.27-3.410.19441430.18651703X-RAY DIFFRACTION99.95
3.41-3.590.20891450.17781731X-RAY DIFFRACTION100
3.59-3.820.17111430.18161701X-RAY DIFFRACTION100
3.82-4.110.16541440.16341717X-RAY DIFFRACTION99.95
4.11-4.530.15821460.15671725X-RAY DIFFRACTION99.95
4.53-5.180.17471460.16661739X-RAY DIFFRACTION100
5.18-6.520.18751460.20181732X-RAY DIFFRACTION99.79
6.53-44.010.17181480.17981771X-RAY DIFFRACTION99.33

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