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- PDB-9ng4: cis-CaaD Y103F mutant apo -

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Basic information

Entry
Database: PDB / ID: 9ng4
Titlecis-CaaD Y103F mutant apo
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: 2.2 Å
AuthorsSilva, K. / Geiger, J.H. / Draths, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: cis-CaaD Y103F mutant apo
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)55,9436
Polymers55,6553
Non-polymers2883
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9020 Å2
ΔGint-103 kcal/mol
Surface area15430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.678, 101.134, 147.297
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
11B-335-

HOH

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Components

#1: Protein Cis-3-chloroacrylic acid dehalogenase


Mass: 18551.582 Da / Num. of mol.: 3 / Mutation: Y103F
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.: 99 / 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: 2.03 Å3/Da / Density % sol: 39.41 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium fluoride 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: Jun 9, 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: 21107 / % possible obs: 89.9 % / Redundancy: 6 % / Biso Wilson estimate: 30.8 Å2 / Rpim(I) all: 0.057 / Net I/σ(I): 9.4
Reflection shellResolution: 2.2→2.24 Å / Num. unique obs: 1056 / Rpim(I) all: 0.277

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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→30.06 Å / SU ML: 0.298 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.3777
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2741 1976 9.85 %
Rwork0.2128 18083 -
obs0.2187 20059 85.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.67 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3423 0 15 99 3537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00863519
X-RAY DIFFRACTIONf_angle_d1.00934764
X-RAY DIFFRACTIONf_chiral_restr0.0577495
X-RAY DIFFRACTIONf_plane_restr0.0088639
X-RAY DIFFRACTIONf_dihedral_angle_d18.28311260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.30051030.2385948X-RAY DIFFRACTION63.81
2.25-2.310.28911260.23431163X-RAY DIFFRACTION78.84
2.31-2.380.31331430.2341237X-RAY DIFFRACTION83.38
2.38-2.460.33381550.23931306X-RAY DIFFRACTION87.33
2.46-2.550.26911380.22881332X-RAY DIFFRACTION88.39
2.55-2.650.29261560.23011274X-RAY DIFFRACTION87.35
2.65-2.770.36031400.22981317X-RAY DIFFRACTION86.99
2.77-2.910.36161300.25121309X-RAY DIFFRACTION86.84
2.91-3.10.33011410.23061303X-RAY DIFFRACTION85.7
3.1-3.340.30611390.23661334X-RAY DIFFRACTION88.73
3.34-3.670.25731430.20571312X-RAY DIFFRACTION86.2
3.67-4.20.26311460.1851360X-RAY DIFFRACTION88.33
4.2-5.290.19321500.17231397X-RAY DIFFRACTION90.73
5.29-30.060.24851660.2161491X-RAY DIFFRACTION92.21

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