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- PDB-9nf9: cis-CaaD E114N mutant apo -

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Basic information

Entry
Database: PDB / ID: 9nf9
Titlecis-CaaD E114N 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: 2.51 Å
AuthorsSilva, K. / Geiger, J.H. / Draths, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: cis-CaaD E114N 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)56,3396
Polymers56,0513
Non-polymers2883
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9070 Å2
ΔGint-104 kcal/mol
Surface area15050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.222, 99.020, 137.557
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: 18683.770 Da / Num. of mol.: 3 / Mutation: E114N
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.: 57 / 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: 1.77 Å3/Da / Density % sol: 30.64 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: (0.03 M citric acid, 0.07 M BIS-TRIS propane) pH 7.6

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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 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.13 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 13174 / % possible obs: 94.3 % / Redundancy: 8.4 % / Biso Wilson estimate: 38.6 Å2 / Rpim(I) all: 0.061 / Net I/σ(I): 12.53
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 664 / Rpim(I) all: 0.318

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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→28.71 Å / SU ML: 0.386 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.634
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2901 1265 10.18 %
Rwork0.215 11165 -
obs0.2227 12430 89.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.17 Å2
Refinement stepCycle: LAST / Resolution: 2.51→28.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3418 0 15 57 3490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143513
X-RAY DIFFRACTIONf_angle_d1.6664759
X-RAY DIFFRACTIONf_chiral_restr0.0796495
X-RAY DIFFRACTIONf_plane_restr0.0157638
X-RAY DIFFRACTIONf_dihedral_angle_d20.32561258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.610.34441190.2451992X-RAY DIFFRACTION72.33
2.61-2.730.45691270.27211177X-RAY DIFFRACTION86.47
2.73-2.880.35861540.24141357X-RAY DIFFRACTION98.37
2.88-3.060.32411520.23681328X-RAY DIFFRACTION97.3
3.06-3.290.31181450.22831274X-RAY DIFFRACTION93.73
3.29-3.620.30361250.22861110X-RAY DIFFRACTION79.37
3.62-4.140.3211330.2181128X-RAY DIFFRACTION80.73
4.14-5.210.22711510.17691367X-RAY DIFFRACTION97.56
5.22-28.710.23461590.19981432X-RAY DIFFRACTION96.78

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