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- PDB-21bk: Crystal Structure of the Fluoroacetate Dehalogenase RPA1163-His28... -

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Basic information

Entry
Database: PDB / ID: 21bk
TitleCrystal Structure of the Fluoroacetate Dehalogenase RPA1163-His280Ala with (S)-2-fluoro-3-phenylpropanoic acid
ComponentsFluoroacetate dehalogenase
KeywordsHYDROLASE / 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: 2.01428242402 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
DepositionDec 6, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 7, 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)67,6312
Polymers67,6312
Non-polymers00
Water7,566420
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-18 kcal/mol
Surface area19870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.226, 76.794, 83.305
Angle α, β, γ (deg.)90.0, 103.595, 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: 33815.422 Da / Num. of mol.: 2 / Mutation: 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 1.9 Å3/Da / Density % sol: 35.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / 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: 0.9785 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: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2→40.4855 Å / Num. obs: 33118 / % possible obs: 97.7 % / Redundancy: 6.59 % / Biso Wilson estimate: 22.9123975818 Å2 / CC1/2: 0.8463 / Net I/σ(I): 6.49
Reflection shellResolution: 2.01→40.48 Å / Num. unique obs: 33118 / CC1/2: 0.8463

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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: 2.01428242402→40.4854601326 Å / SU ML: 0.24354394368 / Cross valid method: NONE / σ(F): 1.35063792323 / Phase error: 23.5596531626
RfactorNum. reflection% reflection
Rfree0.212259180811 2002 6.04651162791 %
Rwork0.153216846434 31108 -
obs0.15683072412 33110 98.8387713066 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.5512613691 Å2
Refinement stepCycle: LAST / Resolution: 2.01428242402→40.4854601326 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4648 0 22 420 5090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008642181963364821
X-RAY DIFFRACTIONf_angle_d1.261422070256560
X-RAY DIFFRACTIONf_chiral_restr0.0477427340206675
X-RAY DIFFRACTIONf_plane_restr0.00629961606587859
X-RAY DIFFRACTIONf_dihedral_angle_d13.41967873341720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0143-2.06470.3441507561671340.239708812422134X-RAY DIFFRACTION94.0688510991
2.0647-2.12050.3411116047491380.20521882442174X-RAY DIFFRACTION99.2274678112
2.1205-2.18290.2523854890181430.1931154575512239X-RAY DIFFRACTION98.5927152318
2.1829-2.25330.2804798513441420.1795562878542192X-RAY DIFFRACTION99.150382328
2.2533-2.33380.2669961381651390.1759500437032217X-RAY DIFFRACTION98.9915966387
2.3338-2.42730.2575242078831420.1690425543882249X-RAY DIFFRACTION98.8833746898
2.4273-2.53770.2120967670531420.1633095365442196X-RAY DIFFRACTION99.5741056218
2.5377-2.67150.2589258688311430.1628476240892215X-RAY DIFFRACTION99.2842105263
2.6715-2.83880.221373524211470.1573219558882240X-RAY DIFFRACTION99.2928452579
2.8388-3.0580.1939722514321460.1477470925492224X-RAY DIFFRACTION99.204688154
3.058-3.36560.1971253291561450.1404301858092243X-RAY DIFFRACTION99.5414756148
3.3656-3.85220.1953136946391440.1235663567382234X-RAY DIFFRACTION99.2073425115
3.8522-4.85210.1469831349251460.1163204752672263X-RAY DIFFRACTION99.7928748964
4.8521-40.480.1750010626661510.1669125446752288X-RAY DIFFRACTION99.1060544494
Refinement TLS params.Method: refined / Origin x: -1.08957909001 Å / Origin y: -4.81595364073 Å / Origin z: 31.781670136 Å
111213212223313233
T0.0793765757665 Å20.00359618213715 Å2-0.00288552956566 Å2-0.0610359910188 Å20.00562058616538 Å2--0.0889992563527 Å2
L0.178298327594 °20.0311863770435 °2-0.14786417236 °2-0.0374985270269 °2-0.0236491188826 °2--0.493726784673 °2
S-0.00816431917344 Å °0.00111035118506 Å °-5.38053313041E-5 Å °-0.00126645951749 Å °0.0108314226169 Å °0.00210115291585 Å °0.0199793023018 Å °-0.00923438068611 Å °-2.91023897699E-6 Å °
Refinement TLS groupSelection details: all

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