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- PDB-9ldq: Crystal Structure of a triple-mutant(F12Y/P84T/F86W) of halohydri... -

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Basic information

Entry
Database: PDB / ID: 9ldq
TitleCrystal Structure of a triple-mutant(F12Y/P84T/F86W) of halohydrin dehalogenase HheC
ComponentsHalohydrin dehalogenase
KeywordsLYASE / halohydrin dehalogenase
Function / homology: / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / Halohydrin dehalogenase
Function and homology information
Biological speciesRhizobium radiobacter (Agrobacterium genomosp. 4)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsWan, N.W. / Hu, D. / Lu, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22167023 China
CitationJournal: To Be Published
Title: Crystal Structure of a triple-mutant(F12Y/P84T/F86W) of halohydrin dehalogenase HheC
Authors: Wan, N.W.
History
DepositionJan 6, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Halohydrin dehalogenase
B: Halohydrin dehalogenase
C: Halohydrin dehalogenase
D: Halohydrin dehalogenase


Theoretical massNumber of molelcules
Total (without water)115,7554
Polymers115,7554
Non-polymers00
Water7,116395
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17450 Å2
ΔGint-114 kcal/mol
Surface area32620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.540, 97.750, 146.580
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
Halohydrin dehalogenase


Mass: 28938.650 Da / Num. of mol.: 4 / Mutation: F12Y/P84T/F86W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium radiobacter (Agrobacterium genomosp. 4)
Gene: hheC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q93D82
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O
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: 2.15 Å3/Da / Density % sol: 42.84 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 2% v/v 1, 4-dioxane, 0.1 M Tris pH 8.0, 15%w/v Polyethylene glycol 3350. 10 mg/mL protein concentration, the growth time is 7 days.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.24→50.45 Å / Num. obs: 49335 / % possible obs: 98.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.38
Reflection shellResolution: 2.24→2.25 Å / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 6.38 / Num. unique obs: 48270

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Processing

Software
NameVersionClassification
PHENIX1.13_2998-000refinement
HKL-3000data scaling
HKL-3000data reduction
AMPLEphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→50.446 Å / SU ML: 0.4 / Cross valid method: NONE / σ(F): 1.96 / Phase error: 33.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2808 2414 5 %
Rwork0.2241 --
obs0.2271 48270 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.24→50.446 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7872 0 0 395 8267
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088088
X-RAY DIFFRACTIONf_angle_d0.90511012
X-RAY DIFFRACTIONf_dihedral_angle_d8.0274788
X-RAY DIFFRACTIONf_chiral_restr0.0511196
X-RAY DIFFRACTIONf_plane_restr0.0061428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2401-2.28580.4851250.46052312X-RAY DIFFRACTION86
2.2858-2.33550.38921260.31052684X-RAY DIFFRACTION100
2.3355-2.38980.36261310.27592697X-RAY DIFFRACTION100
2.3898-2.44960.35011330.25582697X-RAY DIFFRACTION100
2.4496-2.51580.30961450.2512691X-RAY DIFFRACTION100
2.5158-2.58980.30541470.24342697X-RAY DIFFRACTION100
2.5898-2.67340.36621520.26812690X-RAY DIFFRACTION100
2.6734-2.7690.40381450.26732684X-RAY DIFFRACTION100
2.769-2.87980.32971360.2462729X-RAY DIFFRACTION100
2.8798-3.01090.33161360.24532709X-RAY DIFFRACTION100
3.0109-3.16960.32691430.23852717X-RAY DIFFRACTION100
3.1696-3.36810.27131400.22782713X-RAY DIFFRACTION100
3.3681-3.62810.2621410.21542721X-RAY DIFFRACTION99
3.6281-3.99310.27391360.20172682X-RAY DIFFRACTION98
3.9931-4.57060.1981520.1542756X-RAY DIFFRACTION100
4.5706-5.75720.20231680.16372792X-RAY DIFFRACTION100
5.7572-50.440.20831580.17782885X-RAY DIFFRACTION99

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