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- PDB-9ng7: cis-CaaD H28A mutant -

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Basic information

Entry
Database: PDB / ID: 9ng7
Titlecis-CaaD H28A mutant
ComponentsCis-3-chloroacrylic acid dehalogenase
KeywordsHYDROLASE / Tautomerase / cis-CaaD / acetylenecaarboxylic acid
Function / homologyTautomerase, cis-CaaD-like / Putative oxalocrotonate tautomerase enzyme / Tautomerase/MIF superfamily / ACETATE ION / 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 H28A mutant
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)55,6205
Polymers55,5023
Non-polymers1182
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7890 Å2
ΔGint-37 kcal/mol
Surface area13540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.548, 87.682, 153.964
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

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Components

#1: Protein Cis-3-chloroacrylic acid dehalogenase


Mass: 18500.514 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 1.54 Å3/Da / Density % sol: 19.97 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.2 M ammonium acetate 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: 1.8→50 Å / Num. obs: 32217 / % possible obs: 99.5 % / Redundancy: 7.8 % / Biso Wilson estimate: 18.24 Å2 / Rpim(I) all: 0.032 / Net I/σ(I): 27.66
Reflection shellResolution: 1.8→1.83 Å / Num. unique obs: 1575 / Rpim(I) all: 0.346

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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→28.92 Å / SU ML: 0.1678 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.0813
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.231 3005 6.39 %
Rwork0.1897 44045 -
obs0.1923 31857 76.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.17 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2799 0 8 155 2962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00692868
X-RAY DIFFRACTIONf_angle_d0.87833879
X-RAY DIFFRACTIONf_chiral_restr0.0557417
X-RAY DIFFRACTIONf_plane_restr0.0063515
X-RAY DIFFRACTIONf_dihedral_angle_d16.30451032
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.2675850.26581200X-RAY DIFFRACTION43.52
1.82-1.860.3078940.2531320X-RAY DIFFRACTION48.1
1.86-1.890.2178860.24951338X-RAY DIFFRACTION49.15
1.89-1.930.2561930.24181396X-RAY DIFFRACTION50.36
1.93-1.970.2543950.22921407X-RAY DIFFRACTION51.26
1.97-2.010.2594970.21091442X-RAY DIFFRACTION52.24
2.01-2.060.1886940.20721453X-RAY DIFFRACTION52.78
2.06-2.110.24891010.20161571X-RAY DIFFRACTION55.83
2.11-2.160.26211120.18891629X-RAY DIFFRACTION59.97
2.16-2.230.20611430.18121942X-RAY DIFFRACTION70.39
2.23-2.30.21991550.18432250X-RAY DIFFRACTION80.38
2.3-2.380.22351610.18182475X-RAY DIFFRACTION91.81
2.38-2.480.23541860.18862635X-RAY DIFFRACTION98.05
2.48-2.590.25441900.18512761X-RAY DIFFRACTION99.33
2.59-2.730.26641840.18352763X-RAY DIFFRACTION99.56
2.73-2.90.26171830.18892740X-RAY DIFFRACTION100
2.9-3.120.20791910.1952765X-RAY DIFFRACTION99.97
3.12-3.430.25741810.17932723X-RAY DIFFRACTION99.05
3.43-3.930.20911980.17632757X-RAY DIFFRACTION99.86
3.93-4.940.18651860.16652746X-RAY DIFFRACTION99.97
4.95-28.920.24891900.21662732X-RAY DIFFRACTION99.25

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