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- PDB-9o2p: cis-CaaD E114Q mutant with covalent intermediates of the hydratio... -

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Basic information

Entry
Database: PDB / ID: 9o2p
Titlecis-CaaD E114Q mutant with covalent intermediates of the hydration and decarboxylation of cis-3-chloroacrylic acid
Components(Cis-3-chloroacrylic acid ...) x 2
KeywordsHYDROLASE / Tautomerase / cis-CaaD / acetylenecaarboxylic acid
Function / homologyTautomerase, cis-CaaD-like / Putative oxalocrotonate tautomerase enzyme / Tautomerase/MIF superfamily / 3-HYDROXY-PROPANOIC ACID / ACRYLIC ACID / 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 E114Q mutant with covalent intermediates of the hydration and decarboxylation of acetylenecarboxylic acid
Authors: Silva, K. / Geiger, J.H. / Draths, K.
History
DepositionApr 4, 2025Deposition site: RCSB / Processing site: RCSB
SupersessionApr 16, 2025ID: 9NG3
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.1May 14, 2025Group: Structure summary / Category: entity / struct / Item: _entity.pdbx_mutation / _struct.title

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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)55,9846
Polymers55,7263
Non-polymers2583
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9060 Å2
ΔGint-55 kcal/mol
Surface area15430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.608, 101.228, 148.090
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

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Cis-3-chloroacrylic acid ... , 2 types, 3 molecules ABC

#1: Protein Cis-3-chloroacrylic acid dehalogenase


Mass: 18566.598 Da / Num. of mol.: 2 / Mutation: E114Q
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: 18592.635 Da / Num. of mol.: 1 / Mutation: E114Q
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

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Non-polymers , 4 types, 146 molecules

#3: Chemical ChemComp-AKR / ACRYLIC ACID


Mass: 72.063 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H4O2 / Source: (gene. exp.) coryneform bacterium (bacteria) / Gene: cis-caaD / Production host: Escherichia coli (E. coli) / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-3OH / 3-HYDROXY-PROPANOIC ACID


Mass: 90.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H6O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.04 Å3/Da / Density % sol: 39.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: (0.05 citric acid, 0.05 BIS-TRIS propane) pH 5 20% w/v PEG 3,352

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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 29, 2021
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: 21779 / % possible obs: 92.4 % / Redundancy: 7.2 % / Biso Wilson estimate: 29.26 Å2 / Rpim(I) all: 0.037 / Net I/σ(I): 19.14
Reflection shellResolution: 2.2→2.24 Å / Num. unique obs: 964 / Rpim(I) all: 0.325

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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→35.8 Å / SU ML: 0.2733 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.1025
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2363 3087 9.16 %
Rwork0.1726 30611 -
obs0.1783 21185 75.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.13 Å2
Refinement stepCycle: LAST / Resolution: 2.2→35.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3426 0 18 143 3587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00873524
X-RAY DIFFRACTIONf_angle_d0.96124767
X-RAY DIFFRACTIONf_chiral_restr0.0555495
X-RAY DIFFRACTIONf_plane_restr0.0099641
X-RAY DIFFRACTIONf_dihedral_angle_d18.51861266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.3801740.2917701X-RAY DIFFRACTION38.58
2.25-2.260.628930.465755X-RAY DIFFRACTION10.74
2.27-2.310.3432760.2526726X-RAY DIFFRACTION42.41
2.31-2.350.26441060.21381018X-RAY DIFFRACTION54.7
2.35-2.40.26431110.20261033X-RAY DIFFRACTION57.26
2.4-2.440.27231140.19731173X-RAY DIFFRACTION63.49
2.44-2.50.27351280.19871309X-RAY DIFFRACTION70.72
2.5-2.560.28151570.18981447X-RAY DIFFRACTION77.26
2.56-2.620.24681550.18161503X-RAY DIFFRACTION82.65
2.62-2.690.241720.19111622X-RAY DIFFRACTION87.38
2.69-2.770.33591560.19351669X-RAY DIFFRACTION90.35
2.77-2.860.36571810.2291681X-RAY DIFFRACTION90.83
2.86-2.960.24751790.19611730X-RAY DIFFRACTION92.09
2.96-3.080.27771720.19611717X-RAY DIFFRACTION94.97
3.08-3.220.2791590.19841739X-RAY DIFFRACTION93.13
3.22-3.390.25011740.18971715X-RAY DIFFRACTION92.06
3.39-3.60.27531830.17311605X-RAY DIFFRACTION88.47
3.6-3.880.1871200.16191173X-RAY DIFFRACTION63.44
3.88-4.270.18551400.12931492X-RAY DIFFRACTION79.84
4.27-4.880.16841760.13121836X-RAY DIFFRACTION98.72
4.88-6.150.20511770.14951836X-RAY DIFFRACTION98.97
6.15-35.80.18491740.15211831X-RAY DIFFRACTION98.28

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