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- PDB-9ngl: cis-CaaD E114Q -

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Basic information

Entry
Database: PDB / ID: 9ngl
Titlecis-CaaD E114Q
ComponentsCis-3-chloroacrylic acid dehalogenase
KeywordsHYDROLASE / Tautomerase / cis-CaaD
Function / homologyTautomerase, cis-CaaD-like / Putative oxalocrotonate tautomerase enzyme / Tautomerase/MIF superfamily / PHOSPHATE ION / Cis-3-chloroacrylic acid dehalogenase
Function and homology information
Biological speciescoryneform bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSilva, K. / Geiger, J.H. / Draths, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: cis-CaaD E114Q
Authors: Silva, K. / Geiger, J.H. / Draths, K.
History
DepositionFeb 22, 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)55,9856
Polymers55,7003
Non-polymers2853
Water6,972387
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9030 Å2
ΔGint-73 kcal/mol
Surface area15270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.977, 101.078, 144.071
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
11A-375-

HOH

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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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 1.96 Å3/Da / Density % sol: 37.25 %
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 3,354

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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: 1.8→50 Å / Num. obs: 40869 / % possible obs: 99.5 % / Redundancy: 9.8 % / Biso Wilson estimate: 18.84 Å2 / Rpim(I) all: 0.026 / Net I/σ(I): 27.89
Reflection shellResolution: 1.8→1.83 Å / Num. unique obs: 2024 / Rpim(I) all: 0.204

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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: 1.8→29.53 Å / SU ML: 0.1956 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.1833
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2153 1996 4.91 %
Rwork0.1734 38692 -
obs0.1755 40688 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.4 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3433 0 15 387 3835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073551
X-RAY DIFFRACTIONf_angle_d0.99554811
X-RAY DIFFRACTIONf_chiral_restr0.0675499
X-RAY DIFFRACTIONf_plane_restr0.0085645
X-RAY DIFFRACTIONf_dihedral_angle_d5.4626474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.32131430.25262692X-RAY DIFFRACTION97.42
1.84-1.890.25361350.21162682X-RAY DIFFRACTION97.2
1.89-1.950.21581380.18122723X-RAY DIFFRACTION98.76
1.95-2.010.20021410.17772745X-RAY DIFFRACTION99.79
2.01-2.080.2221450.1762737X-RAY DIFFRACTION99.45
2.08-2.170.23951350.18612765X-RAY DIFFRACTION99.76
2.17-2.270.22711500.17042746X-RAY DIFFRACTION99.52
2.27-2.390.20631430.16862759X-RAY DIFFRACTION99.93
2.39-2.530.24751500.17792771X-RAY DIFFRACTION99.66
2.54-2.730.21991380.17862793X-RAY DIFFRACTION99.86
2.73-30.22111460.1792789X-RAY DIFFRACTION99.86
3.01-3.440.21351370.17552758X-RAY DIFFRACTION97.87
3.44-4.330.19241410.14222807X-RAY DIFFRACTION99.13
4.33-29.530.18941540.17182925X-RAY DIFFRACTION99.07

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