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- PDB-2yxp: The Effect of Deuteration on Protein Structure A High Resolution ... -

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Basic information

Entry
Database: PDB / ID: 2yxp
TitleThe Effect of Deuteration on Protein Structure A High Resolution Comparison of Hydrogenous and Perdeuterated Haloalkane Dehalogenase
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / protein deuteration / haloalkane dehalogenase / high resolution structure / catalytic mechanism
Function / homology
Function and homology information


1,2-dichloroethane catabolic process / haloalkane dehalogenase / haloalkane dehalogenase activity / epoxide hydrolase activity / response to toxic substance
Similarity search - Function
Haloalkane dehalogenase, subfamily 1 / : / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Haloalkane dehalogenase
Similarity search - Component
Biological speciesXanthobacter autotrophicus (bacteria)
MethodX-RAY DIFFRACTION / rigid body refinement / Resolution: 1.53 Å
AuthorsLiu, X. / Hanson, L. / Langan, P. / Viola, R.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: The effect of deuteration on protein structure: a high-resolution comparison of hydrogenous and perdeuterated haloalkane dehalogenase.
Authors: Liu, X. / Hanson, B.L. / Langan, P. / Viola, R.E.
History
DepositionApr 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Haloalkane dehalogenase


Theoretical massNumber of molelcules
Total (without water)35,1761
Polymers35,1761
Non-polymers00
Water7,188399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.666, 72.184, 41.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11X-659-

HOH

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Components

#1: Protein Haloalkane dehalogenase


Mass: 35175.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthobacter autotrophicus (bacteria) / Strain: GJ10 / Gene: dhlA / Plasmid: pCH109 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P22643, haloalkane dehalogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / 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: 1.96 Å3/Da / Density % sol: 37.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 2.4M ammonium sulfate, 0.1M MES,, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 13, 2004
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.53→37.62 Å / Num. obs: 36268 / % possible obs: 0.99 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 1.4 / Redundancy: 6.12 % / Rsym value: 0.055 / Net I/σ(I): 17.5
Reflection shellResolution: 1.53→1.59 Å / Redundancy: 2.05 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 1996 / Rsym value: 0.257 / % possible all: 0.48

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: rigid body refinement / Resolution: 1.53→37.62 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.584 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(I): 3.1 / ESU R: 0.092 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18477 1814 5 %RANDOM
Rwork0.15823 ---
obs0.15956 34454 85.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.281 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2--0 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.53→37.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2479 0 0 399 2878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222552
X-RAY DIFFRACTIONr_bond_other_d0.0010.021738
X-RAY DIFFRACTIONr_angle_refined_deg1.2471.9563472
X-RAY DIFFRACTIONr_angle_other_deg0.89534214
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8385309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83524.094127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.71215400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8241515
X-RAY DIFFRACTIONr_chiral_restr0.0810.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022872
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02545
X-RAY DIFFRACTIONr_nbd_refined0.2310.2582
X-RAY DIFFRACTIONr_nbd_other0.1970.21924
X-RAY DIFFRACTIONr_nbtor_refined0.190.21269
X-RAY DIFFRACTIONr_nbtor_other0.0850.21191
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2295
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2020.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.243
X-RAY DIFFRACTIONr_mcbond_it0.971.52002
X-RAY DIFFRACTIONr_mcbond_other0.1591.5614
X-RAY DIFFRACTIONr_mcangle_it1.1522508
X-RAY DIFFRACTIONr_scbond_it1.9831201
X-RAY DIFFRACTIONr_scangle_it2.8534.5964
LS refinement shellResolution: 1.53→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 26 -
Rwork0.313 568 -
obs--19.03 %

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