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- PDB-9nf3: cis-CaaD E114D mutant with a covalent ethylene intermediate of th... -

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Basic information

Entry
Database: PDB / ID: 9nf3
Titlecis-CaaD E114D mutant with a covalent ethylene intermediate of the hydration and decarboxylation of cis-3-chloroacrylic acid
Components(Cis-3-chloroacrylic acid dehalogenase) x 2
KeywordsHYDROLASE / cis-CaaD / tautomerase / acetylenecarboxylic 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: 1.8 Å
AuthorsSilva, K. / Geiger, J.H. / Draths, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: cis-CaaD E114D mutant with a covalent ethylene intermediate of the hydration and decarboxylation of acetylenecarboxylic acid
Authors: Silva, K. / Geiger, J.H. / Draths, K.
History
DepositionFeb 20, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.1May 14, 2025Group: Structure summary / Category: struct / Item: _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)55,9756
Polymers55,6873
Non-polymers2883
Water7,314406
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9050 Å2
ΔGint-107 kcal/mol
Surface area15360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.534, 99.939, 142.794
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
11A-408-

HOH

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Components

#1: Protein Cis-3-chloroacrylic acid dehalogenase


Mass: 18553.557 Da / Num. of mol.: 2 / Mutation: E114D
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: Protein Cis-3-chloroacrylic acid dehalogenase


Mass: 18579.594 Da / Num. of mol.: 1 / Mutation: E114D
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
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 1.91 Å3/Da / Density % sol: 35.5 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.2 M ammonium sulfate 20% w/v PEG 3,353

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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: Jul 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.13 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 36388 / % possible obs: 90.69 % / Redundancy: 6.4 % / Biso Wilson estimate: 23.74 Å2 / Rpim(I) all: 0.037 / Net I/σ(I): 13.3
Reflection shellResolution: 1.8→1.83 Å / Num. unique obs: 1251 / Rpim(I) all: 0.375

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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: 1.8→29.77 Å / SU ML: 0.2114 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.7431
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2238 1973 5.48 %
Rwork0.1804 34045 -
obs0.1828 36018 90.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.39 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3430 0 17 406 3853
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083539
X-RAY DIFFRACTIONf_angle_d1.00574794
X-RAY DIFFRACTIONf_chiral_restr0.0624498
X-RAY DIFFRACTIONf_plane_restr0.0086643
X-RAY DIFFRACTIONf_dihedral_angle_d16.94841269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.36991040.28721703X-RAY DIFFRACTION64.7
1.85-1.90.27631030.24992018X-RAY DIFFRACTION75.83
1.9-1.950.28091420.23262224X-RAY DIFFRACTION84.47
1.95-2.020.26451420.22272429X-RAY DIFFRACTION91.66
2.02-2.090.24761420.19052588X-RAY DIFFRACTION96.6
2.09-2.170.20291590.18732613X-RAY DIFFRACTION98.96
2.17-2.270.23541540.17882632X-RAY DIFFRACTION98.9
2.27-2.390.23481500.18152619X-RAY DIFFRACTION98.44
2.39-2.540.21461510.18542625X-RAY DIFFRACTION98.34
2.54-2.740.25061470.18482594X-RAY DIFFRACTION96.72
2.74-3.010.23411430.18422567X-RAY DIFFRACTION95.19
3.01-3.450.22091500.17042488X-RAY DIFFRACTION92.17
3.45-4.340.18121360.15012398X-RAY DIFFRACTION87.89
4.34-29.770.21061500.17292547X-RAY DIFFRACTION89.6

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