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- PDB-7b73: Insight into the molecular determinants of thermal stability in h... -

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Basic information

Entry
Database: PDB / ID: 7b73
TitleInsight into the molecular determinants of thermal stability in halohydrin dehalogenase HheD2.
ComponentsShort-chain dehydrogenase/reductase SDR
KeywordsLYASE / thermostability / enantioselectivity changes / directed evolution / protein engineering / short-chain dehydrogenase/reductase enzyme superfamily / dehalogenase
Function / homologyEnoyl-(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 / Short-chain dehydrogenase/reductase SDR
Function and homology information
Biological speciesgamma proteobacterium HTCC2207 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.6 Å
AuthorsWessel, J. / Petrillo, G. / Estevez, M. / Bosh, S. / Seeger, M. / Dijkman, W.P. / Hidalgo, A. / Uson, I. / Osuna, S. / Schallmey, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPGC2018-101370-B-100 Spain
CitationJournal: Febs J. / Year: 2021
Title: Insights into the molecular determinants of thermal stability in halohydrin dehalogenase HheD2.
Authors: Wessel, J. / Petrillo, G. / Estevez-Gay, M. / Bosch, S. / Seeger, M. / Dijkman, W.P. / Iglesias-Fernandez, J. / Hidalgo, A. / Uson, I. / Osuna, S. / Schallmey, A.
History
DepositionDec 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 19, 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: Short-chain dehydrogenase/reductase SDR
B: Short-chain dehydrogenase/reductase SDR
C: Short-chain dehydrogenase/reductase SDR
D: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,84510
Polymers104,8324
Non-polymers1,0136
Water12,647702
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12470 Å2
ΔGint-66 kcal/mol
Surface area33470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.022, 94.857, 140.271
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Short-chain dehydrogenase/reductase SDR


Mass: 26208.033 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) gamma proteobacterium HTCC2207 (bacteria)
Gene: GB2207_06463 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1YQT8
#2: Chemical
ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C8H17NO3S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 702 / 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: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Lithium sulfate 0.2 M, CHES 0.1 M pH 9.5, and Na/K tartrate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.6→78.13 Å / Num. obs: 133216 / % possible obs: 95.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 10.3
Reflection shellResolution: 1.84→1.9 Å / Rmerge(I) obs: 0.2 / Num. unique obs: 9541

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XPREPdata reduction
SCALEPACKdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.6→47.47 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.28 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21 7073 5.1 %RANDOM
Rwork0.174 ---
obs0.176 130371 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 239.45 Å2 / Biso mean: 25.55 Å2 / Biso min: 13.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å20 Å20 Å2
2---0.61 Å20 Å2
3----0.94 Å2
Refinement stepCycle: final / Resolution: 1.6→47.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6961 0 64 702 7727
Biso mean--32.32 40.08 -
Num. residues----922
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0137163
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176756
X-RAY DIFFRACTIONr_angle_refined_deg1.7641.6459724
X-RAY DIFFRACTIONr_angle_other_deg1.4831.58415681
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6875915
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.78422.679336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.612151154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4231541
X-RAY DIFFRACTIONr_chiral_restr0.0990.2952
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028024
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021411
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_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 496 -
Rwork0.346 9541 -
all-10037 -
obs--99.97 %

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