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- PDB-4n2x: Crystal Structure of DL-2-haloacid dehalogenase -

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Basic information

Entry
Database: PDB / ID: 4n2x
TitleCrystal Structure of DL-2-haloacid dehalogenase
ComponentsDL-2-haloacid dehalogenase
KeywordsHYDROLASE / dehalogenases
Function / homology2-haloacid dehalogenase (configuration-inverting) / 2-haloacid dehalogenase (configuration-inverting) activity / DL-2-haloacid dehalogenase
Function and homology information
Biological speciesMethylobacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 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 6, 2013Deposition site: RCSB / 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)205,53018
Polymers204,4256
Non-polymers1,10512
Water51,9192882
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18490 Å2
ΔGint-44 kcal/mol
Surface area59080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.568, 182.568, 112.015
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein
DL-2-haloacid dehalogenase


Mass: 34070.852 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylobacterium (bacteria) / Strain: CPA1 / Gene: dl-dex / Production host: Escherichia coli (E. coli)
References: UniProt: A6BM74, 2-haloacid dehalogenase (configuration-inverting)
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2882 / 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: 2.64 Å3/Da / Density % sol: 53.34 % / Mosaicity: 0.217 °
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5 / Details: pH 7.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 231915 / % possible obs: 100 % / Redundancy: 8 % / Rmerge(I) obs: 0.08 / Χ2: 1.237 / Net I/σ(I): 10.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.767.40.308230570.851100
1.76-1.837.50.259231260.9261100
1.83-1.917.70.21231271.0191100
1.91-2.027.90.166231371.1761100
2.02-2.148.10.135231541.3441100
2.14-2.318.20.108231511.4131100
2.31-2.548.20.09232081.3781100
2.54-2.918.30.068231881.2851100
2.91-3.668.30.047232741.3241100
3.66-508.20.042234931.557199.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.386 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1718 23015 9.9 %RANDOM
Rwork0.1352 ---
obs0.1388 231883 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.52 Å2 / Biso mean: 12.8367 Å2 / Biso min: 3.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20.25 Å2-0 Å2
2--0.49 Å2-0 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14268 0 72 2882 17222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.01914818
X-RAY DIFFRACTIONr_angle_refined_deg2.5651.96520148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75851826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63923.127710
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.219152477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.94615139
X-RAY DIFFRACTIONr_chiral_restr0.1530.22200
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.02111425
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 1604 -
Rwork0.169 14917 -
all-16521 -
obs--98.21 %

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