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- PDB-1s0y: The structure of trans-3-chloroacrylic acid dehalogenase, covalen... -

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Basic information

Entry
Database: PDB / ID: 1s0y
TitleThe structure of trans-3-chloroacrylic acid dehalogenase, covalently inactivated by the mechanism-based inhibitor 3-bromopropiolate at 2.3 Angstrom resolution
Components
  • alpha-subunit of trans-3-chloroacrylic acid dehalogenase
  • beta-subunit of trans-3-chloroacrylic acid dehalogenase
KeywordsLYASE / dehalogenase / tautomerase family / covalent modification / inhibition / Michael addition / dehalogenation mechanism / malonyl inhibitor
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
MALONIC ACID / 2-hydroxymuconate tautomerase / 2-hydroxymuconate tautomerase
Similarity search - Component
Biological speciesPseudomonas pavonaceae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
Authorsde Jong, R.M. / Brugman, W. / Poelarends, G.J. / Whitman, C.P. / Dijkstra, B.W.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The X-ray structure of trans-3-chloroacrylic acid dehalogenase reveals a novel hydration mechanism in the tautomerase superfamily
Authors: de Jong, R.M. / Brugman, W. / Poelarends, G.J. / Whitman, C.P. / Dijkstra, B.W.
History
DepositionJan 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 29, 2015Group: Non-polymer description
Revision 1.4Aug 23, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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)97,43118
Polymers96,80712
Non-polymers6246
Water3,081171
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)48,7169
Polymers48,4036
Non-polymers3123
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14140 Å2
ΔGint-76 kcal/mol
Surface area12480 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)48,7169
Polymers48,4036
Non-polymers3123
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13790 Å2
ΔGint-76 kcal/mol
Surface area12820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.379, 100.637, 69.850
Angle α, β, γ (deg.)90.00, 98.87, 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) / Strain: 170 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EV85
#2: Protein
beta-subunit of trans-3-chloroacrylic acid dehalogenase


Mass: 7647.767 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas pavonaceae (bacteria) / Strain: 170 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EV84
#3: Chemical
ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 22% (w/v) PEG 4000, 100mM Sodium Acetate, 0.15 ammonium Acetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
222 %(w/v)PEG40001reservoir
3100 mMsodium acetate1reservoirpH4.8
40.15 Mammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.57 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Oct 10, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.57 Å / Relative weight: 1
ReflectionResolution: 2.26→35 Å / Num. all: 35250 / Num. obs: 34262 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 9.1 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.072 / Net I/σ(I): 11.2
Reflection shellResolution: 2.26→2.34 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 2.95 / Num. unique all: 2818 / Rsym value: 0.275 / % possible all: 80.6
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 35 Å / Num. obs: 35250 / % possible obs: 98.8 % / Num. measured all: 330560
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.38 Å / % possible obs: 95.2 % / Mean I/σ(I) obs: 3

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OTF

1otf


Resolution: 2.3→34.51 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1420461.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1700 5.1 %RANDOM
Rwork0.222 ---
obs0.222 33258 98.8 %-
all-34958 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.7407 Å2 / ksol: 0.357104 e/Å3
Displacement parametersBiso mean: 21.4 Å2
Baniso -1Baniso -2Baniso -3
1-12.04 Å20 Å20.06 Å2
2---3.26 Å20 Å2
3----8.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.3→34.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5324 0 36 171 5531
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it1.932
X-RAY DIFFRACTIONc_scbond_it1.992
X-RAY DIFFRACTIONc_scangle_it2.742.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.328 244 4.6 %
Rwork0.278 5092 -
obs-2818 95.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5INH.PARAMINH.TOP
Software
*PLUS
Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 35 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.26
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76

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