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- PDB-9yrj: Cis-CaaD E114Q mutant with a covalent hydroxypropionate intermedi... -

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Basic information

Entry
Database: PDB / ID: 9yrj
TitleCis-CaaD E114Q mutant with a covalent hydroxypropionate intermediate of the hydration of acetylenecarboxylic acid
ComponentsCis-3-chloroacrylic acid dehalogenase
KeywordsHYDROLASE / cis-CaaD / tautomerase / acetylenecarboxylic acid
Function / homologyTautomerase, cis-CaaD-like / Putative oxalocrotonate tautomerase enzyme / Tautomerase/MIF superfamily / 3-HYDROXY-PROPANOIC ACID / Cis-3-chloroacrylic acid dehalogenase
Function and homology information
Biological speciescoryneform bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsSilva, K. / Geiger, J.H. / Draths, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: cis-CaaD E114Q mutant with a covalent hydroxypropionate intermediate of the hydration of acetylenecarboxylic acid
Authors: Silva, K. / Geiger, J.H. / Draths, K.
History
DepositionOct 16, 2025Deposition site: RCSB / Processing site: RCSB
SupersessionOct 29, 2025ID: 9O2O
Revision 1.0Oct 29, 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)55,9706
Polymers55,7003
Non-polymers2703
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.374, 100.420, 147.177
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: 18566.598 Da / Num. of mol.: 3 / 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: Chemical ChemComp-3OH / 3-HYDROXY-PROPANOIC ACID


Mass: 90.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2 Å3/Da / Density % sol: 38.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: (0.05 M citric acid, 0.05 M BIS-TRIS propane) pH 5 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: Jul 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.13 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 30885 / % possible obs: 90 % / Redundancy: 5.7 % / Biso Wilson estimate: 19.22 Å2 / Rpim(I) all: 0.027 / Net I/σ(I): 19.59
Reflection shellResolution: 1.93→1.96 Å / Num. unique obs: 1638 / Rpim(I) all: 0.207

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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: 1.93→35.6 Å / SU ML: 0.2223 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.6065
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2398 2039 6.69 %
Rwork0.2196 28433 -
obs0.2209 30472 88.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.68 Å2
Refinement stepCycle: LAST / Resolution: 1.93→35.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3426 0 18 215 3659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01423537
X-RAY DIFFRACTIONf_angle_d1.12754784
X-RAY DIFFRACTIONf_chiral_restr0.0748496
X-RAY DIFFRACTIONf_plane_restr0.0072645
X-RAY DIFFRACTIONf_dihedral_angle_d15.9851276
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.970.28841340.26151796X-RAY DIFFRACTION85.13
1.97-2.020.30031350.24021942X-RAY DIFFRACTION90.82
2.02-2.070.27411400.2331849X-RAY DIFFRACTION89.19
2.07-2.130.25571320.24231966X-RAY DIFFRACTION93.49
2.14-2.20.29671430.23872011X-RAY DIFFRACTION94.93
2.2-2.280.27141370.23961882X-RAY DIFFRACTION89.38
2.28-2.370.25021510.23321986X-RAY DIFFRACTION94.18
2.37-2.480.25211380.23371974X-RAY DIFFRACTION93.45
2.48-2.610.27791420.22671956X-RAY DIFFRACTION91.82
2.61-2.780.24671360.23881887X-RAY DIFFRACTION88.3
2.78-2.990.26181350.23061908X-RAY DIFFRACTION89.72
2.99-3.290.23221330.24551872X-RAY DIFFRACTION87.33
3.29-3.770.21321100.21021601X-RAY DIFFRACTION73.88
3.77-4.740.19921380.17511883X-RAY DIFFRACTION86.92
4.75-35.60.19071350.1851920X-RAY DIFFRACTION84.26

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