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- PDB-9ytu: cis-CaaD E114D mutant with a covalent intermediates of the hydrat... -

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Basic information

Entry
Database: PDB / ID: 9ytu
Titlecis-CaaD E114D mutant with a covalent intermediates of the hydration of acetylenecarboxylic acid
Components(Cis-3-chloroacrylic acid dehalogenase) x 3
KeywordsHYDROLASE / cis-CaaD. acetylenecarboxylic acid / tautomerase
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: 2.51 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 intermediates of the hydration of acetylenecarboxylic acid
Authors: Silva, K. / Geiger, J.H. / Draths, K.
History
DepositionOct 21, 2025Deposition site: RCSB / Processing site: RCSB
SupersessionNov 5, 2025ID: 9NER
Revision 1.0Nov 5, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9135
Polymers55,7733
Non-polymers1402
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8510 Å2
ΔGint-48 kcal/mol
Surface area15540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.256, 98.828, 142.409
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: 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
#2: Protein Cis-3-chloroacrylic acid dehalogenase


Mass: 18639.604 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: Protein Cis-3-chloroacrylic acid dehalogenase


Mass: 18553.557 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
#4: Chemical ChemComp-A1BXY / prop-2-ynoic acid


Mass: 70.047 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 1.9 Å3/Da / Density % sol: 35.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.2 M ammonium sulfate 20% w/v PEG 3,360

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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 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 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 14718 / % possible obs: 98.1 % / Redundancy: 8.7 % / Biso Wilson estimate: 37.49 Å2 / Rpim(I) all: 0.053 / Net I/σ(I): 13.78
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 691 / Rpim(I) all: 0.335

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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: 2.51→35.6 Å / SU ML: 0.3481 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.6744
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.26 1428 10.06 %
Rwork0.1876 12768 -
obs0.1948 14196 94.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.05 Å2
Refinement stepCycle: LAST / Resolution: 2.51→35.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3423 0 18 94 3535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813521
X-RAY DIFFRACTIONf_angle_d0.83964762
X-RAY DIFFRACTIONf_chiral_restr0.0506495
X-RAY DIFFRACTIONf_plane_restr0.008642
X-RAY DIFFRACTIONf_dihedral_angle_d18.07211264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.60.36361100.2618956X-RAY DIFFRACTION73.16
2.6-2.70.36281390.23111258X-RAY DIFFRACTION94.2
2.7-2.820.35141360.21841315X-RAY DIFFRACTION99.25
2.82-2.970.29441470.19971307X-RAY DIFFRACTION98.18
2.97-3.160.2971480.21611329X-RAY DIFFRACTION98.86
3.16-3.40.28331510.2051335X-RAY DIFFRACTION99.07
3.4-3.740.27131510.17071248X-RAY DIFFRACTION94.34
3.74-4.280.2051420.15641292X-RAY DIFFRACTION95.41
4.28-5.390.19371490.15161338X-RAY DIFFRACTION97.51
5.39-35.60.24651550.19881390X-RAY DIFFRACTION96.74

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