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- PDB-2flz: The X-ray structure of cis-3-chloroacrylic acid dehalogenase (cis... -

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Basic information

Entry
Database: PDB / ID: 2flz
TitleThe X-ray structure of cis-3-chloroacrylic acid dehalogenase (cis-CaaD) with a sulfate ion bound in the active site
Componentscis-3-chloroacrylic acid dehalogenase
KeywordsHYDROLASE / 3-chloroacrylic acid dehalogenase / 4OT / hydratase / dehalogenation / 4-oxalocrotonate tautomerase
Function / homologyTautomerase, cis-CaaD-like / Putative oxalocrotonate tautomerase enzyme / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta / : / Cis-3-chloroacrylic acid dehalogenase
Function and homology information
Biological speciescoryneform bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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, W.H. / Kim, Y.J. / Burks, E.A. / Serrano, H. / Thunnissen, A.-M.W.H. / 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_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
Remark 999SEQUENCE THE AUTHOR MAINTAINS THAT THIS IS AN ERROR IN THE SEQUENCE DATABASE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,1806
Polymers49,8923
Non-polymers2883
Water28816
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)50,1806
Polymers49,8923
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area8770 Å2
ΔGint-107 kcal/mol
Surface area16020 Å2
MethodPISA, PQS
2
B: cis-3-chloroacrylic acid dehalogenase
hetero molecules

B: cis-3-chloroacrylic acid dehalogenase
hetero molecules

B: cis-3-chloroacrylic acid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1806
Polymers49,8923
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_546z,x-1,y+11
crystal symmetry operation9_645y+1,z-1,x1
Buried area8740 Å2
ΔGint-106 kcal/mol
Surface area15630 Å2
MethodPISA, PQS
3
C: cis-3-chloroacrylic acid dehalogenase
hetero molecules

C: cis-3-chloroacrylic acid dehalogenase
hetero molecules

C: cis-3-chloroacrylic acid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1806
Polymers49,8923
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_546z,x-1,y+11
crystal symmetry operation9_645y+1,z-1,x1
Buried area8780 Å2
ΔGint-109 kcal/mol
Surface area15510 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)140.763, 140.763, 140.763
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
DetailsThe biological unit is a trimer. The ASU contains three monomers, which form three trimers by rotation around 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.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) coryneform bacterium (bacteria) / Plasmid: pBAD / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: GenBank: 37702690, UniProt: Q6VPE5*PLUS, Hydrolases; Acting on halide bonds; In carbon-halide compounds
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 4.66 Å3/Da / Density % sol: 73.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: equal amounts of protein solution (10 mg/mL) and well solution containing 10% (v/v) 2-propanol as a precipitant, 100 mM phosphate-citrate buffer, pH 4.2, and 0.2 M Li2SO4, VAPOR DIFFUSION, ...Details: equal amounts of protein solution (10 mg/mL) and well solution containing 10% (v/v) 2-propanol as a precipitant, 100 mM phosphate-citrate buffer, pH 4.2, and 0.2 M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 10, 2005 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.75→40 Å / Num. all: 24413 / Num. obs: 24413 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 90 Å2 / Rsym value: 0.093 / Net I/σ(I): 19.2
Reflection shellResolution: 2.75→2.87 Å / Mean I/σ(I) obs: 3.5 / Num. unique all: 1222 / Rsym value: 0.359 / % 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: cis-3-chloroacrylic acid dehalogenase inactivated (1FLT)

1flt


Resolution: 2.75→39.04 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 3763590.05 / Data cutoff high rms absF: 3763590.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1255 5.1 %RANDOM
Rwork0.208 ---
obs0.208 24413 99.9 %-
all-24413 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 19.9622 Å2 / ksol: 0.328788 e/Å3
Displacement parametersBiso mean: 42.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.75→39.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3436 0 15 16 3467
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it2.022
X-RAY DIFFRACTIONc_scbond_it2.12
X-RAY DIFFRACTIONc_scangle_it3.262.5
LS refinement shellResolution: 2.75→2.92 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.381 230 5.7 %
Rwork0.313 3790 -
obs-1222 99.6 %
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

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