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- PDB-3ej3: Structural and mechanistic analysis of trans-3-chloroacrylic acid... -

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Basic information

Entry
Database: PDB / ID: 3ej3
TitleStructural and mechanistic analysis of trans-3-chloroacrylic acid dehalogenase activity
Components
  • Alpha-subunit of trans-3-chloroacrylic acid dehalogenase
  • Beta-subunit of trans-3-chloroacrylic acid dehalogenase
KeywordsHYDROLASE / trans-3-chloroacrylic acid dehalogenase / CaaD / dehalogenase / Isomerase
Function / homology
Function and homology information


2-hydroxymuconate tautomerase / isomerase activity
Similarity search - Function
4-oxalocrotonate tautomerase / Tautomerase enzyme / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / PHOSPHATE ION / 2-hydroxymuconate tautomerase / 2-hydroxymuconate tautomerase
Similarity search - Component
Biological speciesPseudomonas pavonaceae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPegan, S. / Serrano, H. / Whitman, C.P. / Mesecar, A.D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structural and mechanistic analysis of trans-3-chloroacrylic acid dehalogenase activity.
Authors: Pegan, S.D. / Serrano, H. / Whitman, C.P. / Mesecar, A.D.
History
DepositionSep 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-subunit of trans-3-chloroacrylic acid dehalogenase
B: Beta-subunit of trans-3-chloroacrylic acid dehalogenase
C: Alpha-subunit of trans-3-chloroacrylic acid dehalogenase
D: Beta-subunit of trans-3-chloroacrylic acid dehalogenase
E: Alpha-subunit of trans-3-chloroacrylic acid dehalogenase
F: Beta-subunit of trans-3-chloroacrylic acid dehalogenase
G: Alpha-subunit of trans-3-chloroacrylic acid dehalogenase
H: Beta-subunit of trans-3-chloroacrylic acid dehalogenase
I: Alpha-subunit of trans-3-chloroacrylic acid dehalogenase
J: Beta-subunit of trans-3-chloroacrylic acid dehalogenase
K: Alpha-subunit of trans-3-chloroacrylic acid dehalogenase
L: Beta-subunit of trans-3-chloroacrylic acid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,56420
Polymers96,02012
Non-polymers5448
Water10,088560
1
A: Alpha-subunit of trans-3-chloroacrylic acid dehalogenase
B: Beta-subunit of trans-3-chloroacrylic acid dehalogenase
C: Alpha-subunit of trans-3-chloroacrylic acid dehalogenase
D: Beta-subunit of trans-3-chloroacrylic acid dehalogenase
E: Alpha-subunit of trans-3-chloroacrylic acid dehalogenase
F: Beta-subunit of trans-3-chloroacrylic acid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,28210
Polymers48,0106
Non-polymers2724
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14940 Å2
ΔGint-83.2 kcal/mol
Surface area13650 Å2
MethodPISA
2
G: Alpha-subunit of trans-3-chloroacrylic acid dehalogenase
H: Beta-subunit of trans-3-chloroacrylic acid dehalogenase
I: Alpha-subunit of trans-3-chloroacrylic acid dehalogenase
J: Beta-subunit of trans-3-chloroacrylic acid dehalogenase
K: Alpha-subunit of trans-3-chloroacrylic acid dehalogenase
L: Beta-subunit of trans-3-chloroacrylic acid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,28210
Polymers48,0106
Non-polymers2724
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14860 Å2
ΔGint-80 kcal/mol
Surface area13600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.696, 97.314, 69.022
Angle α, β, γ (deg.)90.00, 96.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Alpha-subunit of trans-3-chloroacrylic acid dehalogenase


Mass: 8486.701 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas pavonaceae (bacteria) / Gene: caaD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EV85
#2: Protein
Beta-subunit of trans-3-chloroacrylic acid dehalogenase


Mass: 7516.571 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas pavonaceae (bacteria) / Gene: caaD2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EV84
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 560 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 3350, 0.1 M Bis Tris pH 6.5, 0.1 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→68.7 Å / Num. obs: 70963 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.7→1.76 Å / % possible all: 82.4

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S0Y

1s0y


Resolution: 1.7→68.68 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.297 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21821 3599 5.1 %RANDOM
Rwork0.17916 ---
all0.18115 70924 --
obs0.18115 67363 96.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.36 Å20 Å2-0.61 Å2
2--0.02 Å20 Å2
3----1.51 Å2
Refinement stepCycle: LAST / Resolution: 1.7→68.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5819 0 34 560 6413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225963
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.968065
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1865765
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.27823.404282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.345151060
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8261558
X-RAY DIFFRACTIONr_chiral_restr0.1180.2911
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024490
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.23020
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.24113
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2557
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.2127
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.240
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0851.53835
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.71226017
X-RAY DIFFRACTIONr_scbond_it2.65232334
X-RAY DIFFRACTIONr_scangle_it4.2324.52030
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 206 -
Rwork0.24 3984 -
obs--78.07 %

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