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- PDB-9ngd: cis-CaaD/Cg10062 chimera -

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Basic information

Entry
Database: PDB / ID: 9ngd
Titlecis-CaaD/Cg10062 chimera
ComponentsCis-3-chloroacrylic acid dehalogenase,4-oxalocrotonate tautomerase
KeywordsHYDROLASE / Tautomerase / cis-CaaD / acetylenecaarboxylic acid
Function / homologyTautomerase, cis-CaaD-like / Putative oxalocrotonate tautomerase enzyme / Tautomerase/MIF superfamily / 4-oxalocrotonate tautomerase / Cis-3-chloroacrylic acid dehalogenase
Function and homology information
Biological speciescoryneform bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSilva, K. / Geiger, J.H. / Draths, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: cis-CaaD/Cg10062 chimera
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

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Assembly

Deposited unit
A: Cis-3-chloroacrylic acid dehalogenase,4-oxalocrotonate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5312
Polymers18,4961
Non-polymers351
Water18010
1
A: Cis-3-chloroacrylic acid dehalogenase,4-oxalocrotonate tautomerase
hetero molecules

A: Cis-3-chloroacrylic acid dehalogenase,4-oxalocrotonate tautomerase
hetero molecules

A: Cis-3-chloroacrylic acid dehalogenase,4-oxalocrotonate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5936
Polymers55,4873
Non-polymers1063
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area8290 Å2
ΔGint-67 kcal/mol
Surface area13900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.828, 59.828, 57.111
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-309-

HOH

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Components

#1: Protein Cis-3-chloroacrylic acid dehalogenase,4-oxalocrotonate tautomerase


Mass: 18495.596 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) coryneform bacterium (bacteria) / Gene: cis-caaD, AUP69_07050, AUP70_06515 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6VPE5, UniProt: A0A0S2T163
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 1.6 Å3/Da / Density % sol: 22.9 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.2 M lithium chloride 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: 0.98 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 2758 / % possible obs: 83.3 % / Redundancy: 4.9 % / Biso Wilson estimate: 34.75 Å2 / Rpim(I) all: 0.059 / Net I/σ(I): 12.27
Reflection shellResolution: 2.7→2.75 Å / Num. unique obs: 160 / Rpim(I) all: 0.143

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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: 2.7→38.37 Å / SU ML: 0.3646 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.2263
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3361 482 10.17 %
Rwork0.2394 4256 -
obs0.2492 2751 74.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.73 Å2
Refinement stepCycle: LAST / Resolution: 2.7→38.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms959 0 1 10 970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089981
X-RAY DIFFRACTIONf_angle_d1.18931326
X-RAY DIFFRACTIONf_chiral_restr0.0563141
X-RAY DIFFRACTIONf_plane_restr0.0101176
X-RAY DIFFRACTIONf_dihedral_angle_d17.8783355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-3.080.31051920.28711657X-RAY DIFFRACTION86.85
3.08-3.870.34421900.22111637X-RAY DIFFRACTION86.71
3.88-38.370.3451000.2275962X-RAY DIFFRACTION49.51

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