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- PDB-2flt: The X-ray structure of the cis-3-chloroacrylic acid dehalogenase ... -

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Basic information

Entry
Database: PDB / ID: 2flt
TitleThe X-ray structure of the cis-3-chloroacrylic acid dehalogenase cis-CaaD inactivated with (R)-Oxirane-2-carboxylate
Componentscis-3-chloroacrylic acid dehalogenase
KeywordsHYDROLASE / 3-chloroacrylic acid dehalogenase / 4OT family / hydratase / covalent inhibitor / 4-oxalocrotonate tautomerase
Function / homology
Function and homology information


Tautomerase, cis-CaaD-like / Putative oxalocrotonate tautomerase enzyme / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
LACTIC ACID / : / Cis-3-chloroacrylic acid dehalogenase
Similarity search - Component
Biological speciescoryneform bacterium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
Authorsde Jong, R.M.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystal Structures of Native and Inactivated cis-3-Chloroacrylic Acid Dehalogenase: STRUCTURAL BASIS FOR SUBSTRATE SPECIFICITY AND INACTIVATION BY (R)-OXIRANE-2-CARBOXYLATE.
Authors: de Jong, R.M. / Bazzacco, P. / Poelarends, G.J. / Johnson Jr., W.H. / Kim, Y.J. / Burks, E.A. / Serrano, H. / Thunnissen, A.M. / Whitman, C.P. / Dijkstra, B.W.
History
DepositionJan 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cis-3-chloroacrylic acid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7212
Polymers16,6311
Non-polymers901
Water1,08160
1
A: cis-3-chloroacrylic acid dehalogenase
hetero molecules

A: cis-3-chloroacrylic acid dehalogenase
hetero molecules

A: cis-3-chloroacrylic acid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1626
Polymers49,8923
Non-polymers2703
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area7130 Å2
ΔGint-37 kcal/mol
Surface area12620 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)59.457, 59.457, 57.909
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-1060-

HOH

21A-1061-

HOH

DetailsThe biological unit is a trimer that can be obtained by rotation of the monomer aropund the crystallographic three-fold symmetry axis.

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Components

#1: Protein cis-3-chloroacrylic acid dehalogenase


Mass: 16630.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) coryneform bacterium (bacteria) / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): E. coli BL21 (DE3)
References: GenBank: 37702690, UniProt: Q6VPE5*PLUS, Hydrolases; Acting on halide bonds; In carbon-halide compounds
#2: Chemical ChemComp-LAC / LACTIC ACID


Mass: 90.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 1.78 Å3/Da / Density % sol: 30.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: equal amounts of protein solution (10 mg/mL) and well solution containing 1.6 M potassium sodium phosphate and 100 mM HEPES buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Feb 12, 2004 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 6850 / Num. obs: 6850 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 5.3 Å2 / Rsym value: 0.103 / Net I/σ(I): 19.8
Reflection shellResolution: 2.1→2.2 Å / Mean I/σ(I) obs: 5.5 / Rsym value: 0.355 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: trans-3-chloroacrylic acid dehalogenase (CaaD, PDB ID: 1S0Y)

1s0y


Resolution: 2.1→28.96 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1348806.24 / Data cutoff high rms absF: 1348806.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 327 4.8 %RANDOM
Rwork0.204 ---
all-6850 --
obs-6850 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.0537 Å2 / ksol: 0.391163 e/Å3
Displacement parametersBiso mean: 16 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å22.85 Å20 Å2
2--1.54 Å20 Å2
3----3.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 2.1→28.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms890 0 6 60 956
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_d25.1
X-RAY DIFFRACTIONc_improper_angle_d0.64
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it1.692
X-RAY DIFFRACTIONc_scbond_it1.792
X-RAY DIFFRACTIONc_scangle_it2.682.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.262 54 4.8 %
Rwork0.194 1066 -
obs-679 99 %
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.parINH.top

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