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- PDB-9u5x: Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Lys... -

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Basic information

Entry
Database: PDB / ID: 9u5x
TitleCrystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Lys181Met/His280Ala with 2-fluoro-3-phenylpropanoic 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 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
DepositionMar 22, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 21, 2026Provider: 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


Theoretical massNumber of molelcules
Total (without water)66,8422
Polymers66,8422
Non-polymers00
Water12,647702
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-17 kcal/mol
Surface area20930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.91, 78.532, 85.331
Angle α, β, γ (deg.)90.0, 103.542, 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: 33420.934 Da / Num. of mol.: 2 / Mutation: K181M,H280A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris CGA009 (phototrophic)
Gene: RPA1163 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6NAM1, haloacetate dehalogenase
#2: 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
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: 39.63 %
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: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 27, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.47→41.48 Å / Num. obs: 89513 / % possible obs: 88.7 % / Redundancy: 2.53 % / Biso Wilson estimate: 12.3989026808 Å2 / CC1/2: 0.995 / Net I/σ(I): 4.52
Reflection shellResolution: 1.47→1.52 Å / Num. unique obs: 89513 / CC1/2: 0.96

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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: 1.47→41.4793365854 Å / SU ML: 0.120992269941 / Cross valid method: NONE / σ(F): 1.36188219079 / Phase error: 15.7639267021
RfactorNum. reflection% reflection
Rfree0.166759841376 2005 2.23989811536 %
Rwork0.144042844354 87508 -
obs0.144564082371 89513 97.3771811496 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.3679595672 Å2
Refinement stepCycle: LAST / Resolution: 1.47→41.4793365854 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4657 0 22 702 5381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009450979881654850
X-RAY DIFFRACTIONf_angle_d1.362991809296607
X-RAY DIFFRACTIONf_chiral_restr0.0581525344032680
X-RAY DIFFRACTIONf_plane_restr0.00795826789795869
X-RAY DIFFRACTIONf_dihedral_angle_d13.27557443261729
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.50330.2155760754351380.1629586873966158X-RAY DIFFRACTION95.8003651856
1.5033-1.54390.1909637326751350.1549465741856201X-RAY DIFFRACTION96.7771498396
1.5439-1.58940.1707550036771520.1417263416686156X-RAY DIFFRACTION96.9715603382
1.5894-1.64070.1655653413931380.1384396900416225X-RAY DIFFRACTION96.9378427788
1.6407-1.69930.1719987644641390.1398211707026131X-RAY DIFFRACTION96.4022140221
1.6993-1.76740.180924833781430.1461980946686270X-RAY DIFFRACTION97.6846915461
1.7674-1.84780.1643076820171420.1463990746616236X-RAY DIFFRACTION97.6124885216
1.8478-1.94520.1789876530981460.1417532926076288X-RAY DIFFRACTION98.0195003047
1.9452-2.06710.1509198755241450.1412928047766177X-RAY DIFFRACTION96.4601769912
2.0671-2.22670.157924032331460.1414372371546334X-RAY DIFFRACTION98.7052551409
2.2267-2.45070.177859179541440.1508967122566352X-RAY DIFFRACTION98.6634264885
2.4507-2.80530.159252916161400.1539663785986255X-RAY DIFFRACTION97.2032223742
2.8053-3.53410.1905195142461440.1452164082746383X-RAY DIFFRACTION98.9689158453
3.5341-41.470.1444002130141530.1347156050866342X-RAY DIFFRACTION97.1287572903
Refinement TLS params.Method: refined / Origin x: 12.0579113677 Å / Origin y: -0.850405006841 Å / Origin z: 9.20549368594 Å
111213212223313233
T0.0908289717025 Å20.000443419097602 Å2-0.0104060405348 Å2-0.0854634628423 Å2-0.00278041110383 Å2--0.126840334031 Å2
L0.203631832161 °2-0.00736779548986 °2-0.185854857279 °2-0.0498871032539 °20.0375440234448 °2--0.935730893267 °2
S-0.00351149829586 Å °-0.000760701632002 Å °0.0043557175261 Å °0.00590716836568 Å °0.0165259050512 Å °0.00166631933858 Å °0.00451632046427 Å °0.00251674621837 Å °-0.0130202933199 Å °
Refinement TLS groupSelection details: all

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