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- PDB-8xxb: Crystal Structure of a triple-mutant (A69F/M124P/R127G) of halohy... -

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Basic information

Entry
Database: PDB / ID: 8xxb
TitleCrystal Structure of a triple-mutant (A69F/M124P/R127G) of halohydrin dehalogenase HheD8 complexed with chloride
ComponentsShort-chain dehydrogenase/reductase SDR
KeywordsHYDROLASE / halohydrin dehalogenase
Function / homology: / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / Short-chain dehydrogenase/reductase SDR
Function and homology information
Biological speciesThauera aminoaromatica S2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWan, N.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2025
Title: Biocatalytic enantioselective formation and ring-opening of oxetanes.
Authors: Hua, X. / Wang, Y.F. / Jin, X. / Yu, H.Y. / Wang, H.H. / Chen, Y.Z. / Wan, N.W.
History
DepositionJan 18, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7592
Polymers24,7231
Non-polymers351
Water70339
1
A: Short-chain dehydrogenase/reductase SDR
hetero molecules

A: Short-chain dehydrogenase/reductase SDR
hetero molecules

A: Short-chain dehydrogenase/reductase SDR
hetero molecules

A: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,0358
Polymers98,8944
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
crystal symmetry operation12_545x,x-y-1,-z+1/31
Buried area11960 Å2
ΔGint-115 kcal/mol
Surface area29810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.564, 138.564, 66.822
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3

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Components

#1: Protein Short-chain dehydrogenase/reductase SDR / halohydrin dehalogenase hhd8


Mass: 24723.389 Da / Num. of mol.: 1 / Mutation: A69F,R127G,M124P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thauera aminoaromatica S2 (bacteria) / Gene: C665_05478 / Production host: Escherichia coli (E. coli) / References: UniProt: N6YXW4
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.75 Å3/Da / Density % sol: 67.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.8 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: May 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 30538 / % possible obs: 99.75 % / Redundancy: 37.5 % / Biso Wilson estimate: 38.94 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.09077 / Rpim(I) all: 0.01505 / Net I/σ(I): 38.88
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 39 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 9.21 / Num. unique obs: 1476 / CC1/2: 0.992 / Rpim(I) all: 0.09946 / % possible all: 99.39

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→44.64 Å / SU ML: 0.0683 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.8411
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1903 799 2.85 %
Rwork0.1847 27245 -
obs0.1849 28044 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.41 Å2
Refinement stepCycle: LAST / Resolution: 2.4→44.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1641 0 1 39 1681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00741689
X-RAY DIFFRACTIONf_angle_d1.24382304
X-RAY DIFFRACTIONf_chiral_restr0.0718262
X-RAY DIFFRACTIONf_plane_restr0.0091306
X-RAY DIFFRACTIONf_dihedral_angle_d20.2167600
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.550.27561320.27634526X-RAY DIFFRACTION99.55
2.55-2.750.29471340.23744547X-RAY DIFFRACTION99.79
2.75-3.020.18841320.22194528X-RAY DIFFRACTION99.81
3.02-3.460.22511340.20064533X-RAY DIFFRACTION99.91
3.46-4.360.14911350.16664547X-RAY DIFFRACTION99.98
4.36-44.640.16451320.14784564X-RAY DIFFRACTION99.87

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