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- PDB-3ej7: Structural and mechanistic analysis of trans-3-chloroacrylic acid... -

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Basic information

Entry
Database: PDB / ID: 3ej7
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
2-hydroxymuconate tautomerase / 2-hydroxymuconate tautomerase
Similarity search - Component
Biological speciesPseudomonas pavonaceae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)95,59913
Polymers95,50312
Non-polymers961
Water9,980554
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)47,8487
Polymers47,7516
Non-polymers961
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13470 Å2
ΔGint-86 kcal/mol
Surface area13490 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


Theoretical massNumber of molelcules
Total (without water)47,7516
Polymers47,7516
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12910 Å2
ΔGint-75 kcal/mol
Surface area13340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.249, 83.625, 124.063
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 8400.585 Da / Num. of mol.: 6 / Mutation: R8A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas pavonaceae (bacteria) / Gene: caaD1 / Plasmid: pET3a / 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 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EV84
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / Source method: isolated from a natural source / Formula: H2O

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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

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 Lithium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→69.3 Å / Num. all: 49874 / Num. obs: 49874 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→1.97 Å / % possible all: 95.2

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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: 3EJ3

3ej3


Resolution: 1.9→69.3 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.913 / SU B: 8.722 / SU ML: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.195 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26861 2544 5.1 %RANDOM
Rwork0.20207 ---
all0.20539 47330 --
obs0.20539 47330 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.575 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å20 Å2
2--2.89 Å20 Å2
3----2.21 Å2
Refinement stepCycle: LAST / Resolution: 1.9→69.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5328 0 5 554 5887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225416
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.9547302
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2875694
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.26223.725247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.17515981
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6241549
X-RAY DIFFRACTIONr_chiral_restr0.1040.2847
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023987
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.22793
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.23704
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2481
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2330.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7911.53537
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.19425527
X-RAY DIFFRACTIONr_scbond_it2.13932054
X-RAY DIFFRACTIONr_scangle_it3.194.51764
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.946 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 194 -
Rwork0.247 3328 -
obs--95.92 %

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