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- PDB-9ue2: Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Lys... -

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Basic information

Entry
Database: PDB / ID: 9ue2
TitleCrystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Lys181Ser/Trp185Gly/His280Ala with (S)-2-fluoro-3-(4-(trifluoromethyl)phenyl)propanoic acid
ComponentsFluoroacetate dehalogenase
KeywordsTRANSFERASE / Fluoroacetate dehalogenase
Function / homologyhaloacetate dehalogenase / haloacetate dehalogenase activity / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / : / Fluoroacetate dehalogenase
Function and homology information
Biological speciesRhodopseudomonas palustris CGA009 (phototrophic)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.37860295477 Å
AuthorsHuang, H.S. / Zhang, Z.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: A Route to Powerful Biocatalysts: Designing a Gate-based Synergetic Chain through Long-range Conformational Dynamics Analysis
Authors: Huang, H.S. / Zhang, Z.M.
History
DepositionApr 7, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fluoroacetate dehalogenase
B: Fluoroacetate dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4284
Polymers66,9922
Non-polymers4362
Water13,331740
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-19 kcal/mol
Surface area21140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.846, 79.387, 84.884
Angle α, β, γ (deg.)90.0, 103.691, 90.0
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Fluoroacetate dehalogenase


Mass: 33496.004 Da / Num. of mol.: 2 / Mutation: K181S,W185G,H280A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris CGA009 (phototrophic)
Gene: RPA1163 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NAM1, haloacetate dehalogenase
#2: Chemical ChemComp-A1ES3 / 3-[4-(trifluoromethyl)phenyl]propanoic acid


Mass: 218.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H9F3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 740 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.04 Å3/Da / Density % sol: 39.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 100 mM Tris Ph 8.5,200 mM CaCl2, 20% peg 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 VENTURE / Wavelength: 1.54 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Sep 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.37→57.19 Å / Num. obs: 110887 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 10.9780278097 Å2 / CC1/2: 0.804 / Net I/σ(I): 2.6
Reflection shellResolution: 1.38→1.45 Å / Num. unique obs: 110907 / CC1/2: 0.804

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37860295477→40.6570007475 Å / SU ML: 0.128441682357 / Cross valid method: FREE R-VALUE / σ(F): 1.33647690985 / Phase error: 18.1827224241
RfactorNum. reflection% reflection
Rfree0.179767128092 2005 1.80814703256 %
Rwork0.162148586466 108882 -
obs0.162470244502 110887 99.9396146151 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.6686458922 Å2
Refinement stepCycle: LAST / Resolution: 1.37860295477→40.6570007475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4632 0 30 740 5402
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01502788105154827
X-RAY DIFFRACTIONf_angle_d1.643217627296570
X-RAY DIFFRACTIONf_chiral_restr0.109506541078673
X-RAY DIFFRACTIONf_plane_restr0.0100999590575863
X-RAY DIFFRACTIONf_dihedral_angle_d13.86227915131738
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37861-1.41310.2643160651211390.232565293177776X-RAY DIFFRACTION99.9873673573
1.4131-1.45130.2663523425171430.2216949991037734X-RAY DIFFRACTION100
1.4513-1.4940.255495192111440.2079868561957818X-RAY DIFFRACTION99.9623352166
1.494-1.54220.2339344742481380.1945417463287716X-RAY DIFFRACTION99.9363786741
1.5422-1.59730.2004056248771440.1805933279057736X-RAY DIFFRACTION99.9746257295
1.5973-1.66130.1925410913361450.1673603077757770X-RAY DIFFRACTION99.9747379058
1.6613-1.73690.1843316982681400.1658483164467754X-RAY DIFFRACTION99.9746707194
1.7369-1.82850.1861832895061460.1624509696277759X-RAY DIFFRACTION99.9620637329
1.8285-1.9430.1827925790371440.1583592360527750X-RAY DIFFRACTION99.9620108902
1.943-2.09310.1832311561051470.1549155395167798X-RAY DIFFRACTION99.886849384
2.0931-2.30370.1724526041331380.1526077141577764X-RAY DIFFRACTION99.8862343572
2.3037-2.6370.1658340083891460.1594724202547796X-RAY DIFFRACTION99.9874102984
2.637-3.32210.1827082460481430.1590218479957818X-RAY DIFFRACTION99.9497802888
3.3221-40.6570.1417530442841480.1413725861027893X-RAY DIFFRACTION99.727148704
Refinement TLS params.Method: refined / Origin x: -21.2376097205 Å / Origin y: -60.7380824143 Å / Origin z: 114.97426295 Å
111213212223313233
T0.0839773244086 Å2-0.0140152494277 Å2-0.00789311479048 Å2-0.0526171379304 Å2-0.0118165004746 Å2--0.102645582794 Å2
L0.639161381552 °20.01782324323 °2-0.211129001723 °2-0.0699190750058 °2-0.00519924636892 °2--1.04429077026 °2
S-0.0329092300087 Å °0.07236623654 Å °-0.0224351017134 Å °-0.0231579510328 Å °0.0322566827037 Å °-0.0017788538829 Å °-0.0147864702702 Å °0.0396401349832 Å °-0.00205057883555 Å °
Refinement TLS groupSelection details: all

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