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- PDB-9ng5: cis-CaaD Y103F mutant soaked with acetylencarboxylic acid -

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Basic information

Entry
Database: PDB / ID: 9ng5
Titlecis-CaaD Y103F mutant soaked with acetylencarboxylic acid
ComponentsCis-3-chloroacrylic acid dehalogenase
KeywordsHYDROLASE / Tautomerase / cis-CaaD / acetylenecaarboxylic 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: 2.28 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 acetylencarboxylic acid
Authors: Silva, K. / Geiger, J.H. / Draths, K.
History
DepositionFeb 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9436
Polymers55,6553
Non-polymers2883
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8990 Å2
ΔGint-115 kcal/mol
Surface area15730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.259, 101.341, 137.573
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-332-

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: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.89 Å3/Da / Density % sol: 34.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.2 M magnesium sulfate hep-tahydrate 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: 23-ID-D / Wavelength: 1.13 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.13 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. obs: 17389 / % possible obs: 89.2 % / Redundancy: 8.7 % / Biso Wilson estimate: 29.22 Å2 / Rpim(I) all: 0.071 / Net I/σ(I): 7.13
Reflection shellResolution: 2.3→2.34 Å / Num. unique obs: 917 / Rpim(I) all: 0.301

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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: 2.28→29.43 Å / SU ML: 0.5041 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 37.7687
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3539 1605 9.93 %
Rwork0.2344 14566 -
obs0.2464 16171 82.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.48 Å2
Refinement stepCycle: LAST / Resolution: 2.28→29.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3423 0 15 81 3519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00783519
X-RAY DIFFRACTIONf_angle_d0.95154764
X-RAY DIFFRACTIONf_chiral_restr0.0516495
X-RAY DIFFRACTIONf_plane_restr0.0088639
X-RAY DIFFRACTIONf_dihedral_angle_d20.8871260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.360.4341190.29391105X-RAY DIFFRACTION68.65
2.36-2.440.40441420.29061315X-RAY DIFFRACTION84.37
2.44-2.540.41981620.27531387X-RAY DIFFRACTION87.81
2.54-2.650.39281460.27851390X-RAY DIFFRACTION87.97
2.65-2.790.38891620.2641430X-RAY DIFFRACTION90.25
2.79-2.970.40091580.2281428X-RAY DIFFRACTION89.81
2.97-3.20.32971490.23231391X-RAY DIFFRACTION87.3
3.2-3.520.36461380.22671321X-RAY DIFFRACTION82.2
3.52-4.020.32581360.21251116X-RAY DIFFRACTION69.94
4.03-5.070.30911210.19031127X-RAY DIFFRACTION68.84
5.07-29.430.32311720.22961556X-RAY DIFFRACTION91.48

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