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- PDB-9nfd: cis-CaaD E114N mutant with acetylenecarboxylic acid substrate and... -

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Basic information

Entry
Database: PDB / ID: 9nfd
Titlecis-CaaD E114N mutant with acetylenecarboxylic acid substrate and hydration product malonic semialdehyde
ComponentsCis-3-chloroacrylic acid dehalogenase
KeywordsHYDROLASE / Tautomerase / cis-CaaD / acetylenecarboxylic acid
Function / homologyTautomerase, cis-CaaD-like / Putative oxalocrotonate tautomerase enzyme / Tautomerase/MIF superfamily / : / 3-oxidanylidenepropanoic acid / Cis-3-chloroacrylic acid dehalogenase
Function and homology information
Biological speciescoryneform bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSilva, K. / Geiger, J.H. / Draths, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: cis-CaaD E114N mutant with acetylenecarboxylic acid substrate and hydration product malonic semialdehyde
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

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Assembly

Deposited unit
B: Cis-3-chloroacrylic acid dehalogenase
C: Cis-3-chloroacrylic acid dehalogenase
A: Cis-3-chloroacrylic acid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9046
Polymers55,6583
Non-polymers2463
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8500 Å2
ΔGint-44 kcal/mol
Surface area15430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.405, 100.972, 148.185
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: 18552.572 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-FK2 / 3-oxidanylidenepropanoic acid


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#3: Chemical ChemComp-A1BXY / prop-2-ynoic acid


Mass: 70.047 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.03 Å3/Da / Density % sol: 39.4 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.05 M citric acid, 0.05 M BIS-TRIS propane) pH 6 17% w/v PEG 3,355

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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: 2.3→40 Å / Num. obs: 17606 / % possible obs: 85.5 % / Redundancy: 5.9 % / Biso Wilson estimate: 30.59 Å2 / Rpim(I) all: 0.09 / Net I/σ(I): 9.67
Reflection shellResolution: 2.3→2.34 Å / Num. unique obs: 1024 / Rpim(I) all: 0.338

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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: 2.3→35.31 Å / SU ML: 0.3166 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.49
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2758 1730 10.09 %
Rwork0.2038 15410 -
obs0.2112 17140 82.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.1 Å2
Refinement stepCycle: LAST / Resolution: 2.3→35.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3423 0 17 154 3594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083521
X-RAY DIFFRACTIONf_angle_d0.92444763
X-RAY DIFFRACTIONf_chiral_restr0.0514495
X-RAY DIFFRACTIONf_plane_restr0.0089642
X-RAY DIFFRACTIONf_dihedral_angle_d18.49721265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.32251360.2271342X-RAY DIFFRACTION86.33
2.36-2.440.33611620.22691423X-RAY DIFFRACTION94.57
2.44-2.530.30891620.21991475X-RAY DIFFRACTION94.79
2.53-2.630.32371770.2111427X-RAY DIFFRACTION95.42
2.63-2.750.29361510.21811427X-RAY DIFFRACTION92.12
2.75-2.890.29111640.20661422X-RAY DIFFRACTION93.51
2.89-3.070.29011560.19431396X-RAY DIFFRACTION90.55
3.07-3.310.34031390.20971295X-RAY DIFFRACTION83.96
3.31-3.640.25611290.19291139X-RAY DIFFRACTION73.38
3.64-4.170.2436910.1999897X-RAY DIFFRACTION57.04
4.17-5.250.19691430.17371136X-RAY DIFFRACTION72.96
5.25-35.310.27491200.2191031X-RAY DIFFRACTION62.62

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