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- PDB-3wj8: Crystal Structure of DL-2-haloacid dehalogenase mutant with 2-bro... -

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Basic information

Entry
Database: PDB / ID: 3wj8
TitleCrystal Structure of DL-2-haloacid dehalogenase mutant with 2-bromo-2-methylpropionate
ComponentsDL-2-haloacid dehalogenase
KeywordsHYDROLASE / dehalogenases
Function / homology2-haloacid dehalogenase (configuration-inverting) / DL-2 haloacid dehalogenase activity / 2-bromo-2-methylpropanoic acid / DL-2-haloacid dehalogenase
Function and homology information
Biological speciesMethylobacterium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSiwek, A. / Omi, R. / Hirotsu, K. / Jitsumori, K. / Esaki, N. / Kurihara, T. / Paneth, P.
CitationJournal: Arch.Biochem.Biophys. / Year: 2013
Title: Binding modes of DL-2-haloacid dehalogenase revealed by crystallography, modeling and isotope effects studies.
Authors: Siwek, A. / Omi, R. / Hirotsu, K. / Jitsumori, K. / Esaki, N. / Kurihara, T. / Paneth, P.
History
DepositionOct 7, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DL-2-haloacid dehalogenase
B: DL-2-haloacid dehalogenase
D: DL-2-haloacid dehalogenase
E: DL-2-haloacid dehalogenase
F: DL-2-haloacid dehalogenase
G: DL-2-haloacid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,11218
Polymers204,5586
Non-polymers1,55512
Water11,007611
1
A: DL-2-haloacid dehalogenase
B: DL-2-haloacid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7046
Polymers68,1862
Non-polymers5184
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-8 kcal/mol
Surface area22750 Å2
MethodPISA
2
D: DL-2-haloacid dehalogenase
E: DL-2-haloacid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7046
Polymers68,1862
Non-polymers5184
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-6 kcal/mol
Surface area22950 Å2
MethodPISA
3
F: DL-2-haloacid dehalogenase
G: DL-2-haloacid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7046
Polymers68,1862
Non-polymers5184
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-10 kcal/mol
Surface area22860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.309, 186.309, 114.315
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein
DL-2-haloacid dehalogenase


Mass: 34092.922 Da / Num. of mol.: 6 / Mutation: D54H, D194N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylobacterium (bacteria) / Genus: dl-dex / Strain: CPA1Carboxypeptidase A1 / Production host: Escherichia coli (E. coli)
References: UniProt: A6BM74, 2-haloacid dehalogenase (configuration-inverting)
#2: Chemical
ChemComp-B2P / 2-bromo-2-methylpropanoic acid


Mass: 167.001 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H7BrO2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 611 / 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

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5 / Details: pH 7.5, VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→161.35 Å / Num. obs: 61648 / % possible obs: 99.5 %

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Processing

SoftwareName: REFMAC / Version: 5.6.0117 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.86 / SU B: 13.519 / SU ML: 0.271 / Cross valid method: THROUGHOUT / ESU R Free: 0.392 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26863 6204 10.1 %RANDOM
Rwork0.18739 ---
obs0.19561 55442 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.812 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å20.57 Å2-0 Å2
2--1.13 Å2-0 Å2
3----1.7 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14288 0 78 611 14977
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01914784
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.96320099
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08651802
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.07623.013707
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.301152461
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.45615139
X-RAY DIFFRACTIONr_chiral_restr0.1070.22188
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111401
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.701→2.771 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 472 -
Rwork0.258 3978 -
obs--99.96 %

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