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- PDB-9o2n: cis-CaaD Y103F mutant soaked with cis-3-chloroacrylic acid -

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Basic information

Entry
Database: PDB / ID: 9o2n
Titlecis-CaaD Y103F mutant soaked with cis-3-chloroacrylic acid
ComponentsCis-3-chloroacrylic acid dehalogenase
KeywordsHYDROLASE / Tautomerase / cis-CaaD / cis-3-chloroacrylic acid
Function / homologyTautomerase, cis-CaaD-like / Putative oxalocrotonate tautomerase enzyme / Tautomerase/MIF superfamily / Cis-3-chloroacrylic acid dehalogenase
Function and homology information
Biological speciescoryneform bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSilva, K. / Geiger, J.H. / Draths, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: cis-CaaD Y103F mutant soaked with cis-3-chloroacrylic acid
Authors: Silva, K. / Geiger, J.H. / Draths, K.
History
DepositionApr 4, 2025Deposition site: RCSB / Processing site: RCSB
SupersessionApr 16, 2025ID: 9NG6
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cis-3-chloroacrylic acid dehalogenase
B: Cis-3-chloroacrylic acid dehalogenase
C: Cis-3-chloroacrylic acid dehalogenase


Theoretical massNumber of molelcules
Total (without water)55,6553
Polymers55,6553
Non-polymers00
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8580 Å2
ΔGint-45 kcal/mol
Surface area15190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.641, 100.527, 147.025
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-235-

HOH

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Components

#1: Protein Cis-3-chloroacrylic acid dehalogenase


Mass: 18551.582 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) coryneform bacterium (bacteria) / Gene: cis-caaD / Production host: Escherichia coli (E. coli) / References: UniProt: Q6VPE5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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 Å3/Da / Density % sol: 38.47 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium fluoride 20% w/v PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.13 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.13 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 20691 / % possible obs: 88.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 28.73 Å2 / Rpim(I) all: 0.04 / Net I/σ(I): 14.18
Reflection shellResolution: 2.2→2.24 Å / Num. unique obs: 1026 / Rpim(I) all: 0.222

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→30 Å / SU ML: 0.2389 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4104
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2371 3337 9.75 %
Rwork0.194 30872 -
obs0.1983 20511 77.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.32 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3423 0 0 116 3539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00843507
X-RAY DIFFRACTIONf_angle_d0.95784746
X-RAY DIFFRACTIONf_chiral_restr0.0581495
X-RAY DIFFRACTIONf_plane_restr0.0089639
X-RAY DIFFRACTIONf_dihedral_angle_d18.07641260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.2228760.2083803X-RAY DIFFRACTION46.91
2.23-2.260.24571340.1981911X-RAY DIFFRACTION55.7
2.26-2.30.2497750.2299817X-RAY DIFFRACTION49.47
2.3-2.330.3379790.2336697X-RAY DIFFRACTION41.39
2.33-2.370.31451220.21441054X-RAY DIFFRACTION64.94
2.37-2.420.26321120.21331184X-RAY DIFFRACTION69.94
2.42-2.460.27091450.21651274X-RAY DIFFRACTION77.08
2.46-2.510.27421430.22261355X-RAY DIFFRACTION80.71
2.51-2.570.26671320.19671408X-RAY DIFFRACTION83.06
2.57-2.630.29441430.20491373X-RAY DIFFRACTION83.07
2.63-2.690.28261500.21791381X-RAY DIFFRACTION82.14
2.69-2.770.2321580.19961386X-RAY DIFFRACTION82.88
2.77-2.850.27531430.20851369X-RAY DIFFRACTION83.44
2.85-2.940.2741560.19221370X-RAY DIFFRACTION81.17
2.94-3.040.24881430.20151354X-RAY DIFFRACTION81.31
3.04-3.170.25971720.19951372X-RAY DIFFRACTION84.46
3.17-3.310.28011380.19311408X-RAY DIFFRACTION84.2
3.31-3.480.23191540.18951408X-RAY DIFFRACTION83.53
3.48-3.70.22851560.18021340X-RAY DIFFRACTION80.69
3.7-3.990.23891460.18811480X-RAY DIFFRACTION88.61
3.99-4.390.18011580.16461569X-RAY DIFFRACTION93.1
4.39-5.020.2011670.17541533X-RAY DIFFRACTION92.29
5.02-6.310.23491660.20481557X-RAY DIFFRACTION92.98
6.32-300.19631690.2041469X-RAY DIFFRACTION88.25

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