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- PDB-9nga: cis-CaaD T34A mutant soaked with cis-3-chloroacrylic acid -

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Basic information

Entry
Database: PDB / ID: 9nga
Titlecis-CaaD T34A mutant soaked with cis-3-chloroacrylic acid
ComponentsCis-3-chloroacrylic acid dehalogenase
KeywordsHYDROLASE / Tautomerase / cis-CaaD
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: 2.4 Å
AuthorsSilva, K. / Geiger, J.H. / Draths, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: cis-CaaD T34A mutant soaked with cis-3-chloroacrylic acid
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)55,9016
Polymers55,6133
Non-polymers2883
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9130 Å2
ΔGint-110 kcal/mol
Surface area15350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.723, 98.805, 142.619
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
Components on special symmetry positions
IDModelComponents
11C-316-

HOH

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Components

#1: Protein Cis-3-chloroacrylic acid dehalogenase


Mass: 18537.557 Da / Num. of mol.: 3 / Mutation: T34A
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 1.89 Å3/Da / Density % sol: 34.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.2 M ammonium sulfate 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 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 15076 / % possible obs: 88.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 34.8 Å2 / Rpim(I) all: 0.094 / Net I/σ(I): 7.89
Reflection shellResolution: 2.4→2.44 Å / Num. unique obs: 554 / Rpim(I) all: 0.445

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→40.61 Å / SU ML: 0.3587 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.429
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3085 1193 10.04 %
Rwork0.2114 10690 -
obs0.2209 11883 70.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.62 Å2
Refinement stepCycle: LAST / Resolution: 2.4→40.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3420 0 15 39 3474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00773516
X-RAY DIFFRACTIONf_angle_d1.07814761
X-RAY DIFFRACTIONf_chiral_restr0.0556492
X-RAY DIFFRACTIONf_plane_restr0.0102639
X-RAY DIFFRACTIONf_dihedral_angle_d6.3969468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.50.369470.2745451X-RAY DIFFRACTION27.05
2.5-2.610.4081660.271628X-RAY DIFFRACTION37.82
2.61-2.750.36221010.2689857X-RAY DIFFRACTION51.45
2.75-2.920.36251420.25871158X-RAY DIFFRACTION71
2.92-3.150.34411580.25231431X-RAY DIFFRACTION85.25
3.15-3.460.35371770.2161589X-RAY DIFFRACTION94.69
3.46-3.960.28561820.18891623X-RAY DIFFRACTION95.91
3.96-4.990.24951700.16721589X-RAY DIFFRACTION92.48
4.99-40.610.2981500.22161364X-RAY DIFFRACTION76.27

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