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- PDB-2w11: Structure of the L-2-haloacid dehalogenase from Sulfolobus tokodaii -

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Basic information

Entry
Database: PDB / ID: 2w11
TitleStructure of the L-2-haloacid dehalogenase from Sulfolobus tokodaii
Components2-HALOALKANOIC ACID DEHALOGENASE
KeywordsHYDROLASE / HALOACID DEHALOGENASE / HAD
Function / homology
Function and homology information


(S)-2-haloacid dehalogenase / (S)-2-haloacid dehalogenase activity
Similarity search - Function
L-2-Haloacid dehalogenase / Haloacid dehalogenase-like hydrolase / : / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily ...L-2-Haloacid dehalogenase / Haloacid dehalogenase-like hydrolase / : / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
(2S)-2-HYDROXYPROPANOIC ACID / L-2-haloacid dehalogenase
Similarity search - Component
Biological speciesSULFOLOBUS TOKODAII (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRye, C.A. / Isupov, M.N. / Lebedev, A.A. / Littlechild, J.A.
Citation
Journal: Extremophiles / Year: 2009
Title: Biochemical and Structural Studies of a L-Haloacid Dehalogenase from the Thermophilic Archaeon Sulfolobus Tokodaii.
Authors: Rye, C.A. / Isupov, M.N. / Lebedev, A.A. / Littlechild, J.A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2007
Title: An Order-Disorder Twin Crystal of L-2-Haloacid Dehalogenase from Sulfolobus Tokodaii
Authors: Rye, C.A. / Isupov, M.N. / Lebedev, A.A. / Littlechild, J.A.
History
DepositionOct 13, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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: 2-HALOALKANOIC ACID DEHALOGENASE
B: 2-HALOALKANOIC ACID DEHALOGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1454
Polymers47,9652
Non-polymers1802
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-30.7 kcal/mol
Surface area21570 Å2
MethodPQS
Unit cell
Length a, b, c (Å)127.589, 58.082, 51.192
Angle α, β, γ (deg.)90.00, 97.23, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2037-

HOH

21B-2115-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99999, -0.00155, -0.0034), (-0.00155, -1, 0.00125), (-0.0034, -0.00124, -0.99999)
Vector: -0.04745, -17.678, 0.14365)

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Components

#1: Protein 2-HALOALKANOIC ACID DEHALOGENASE / L-HALOACID DEHALOGENASE


Mass: 23982.600 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS TOKODAII (archaea) / Strain: 7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96XE7, (S)-2-haloacid dehalogenase
#2: Chemical ChemComp-2OP / (2S)-2-HYDROXYPROPANOIC ACID


Mass: 90.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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 %
Description: THE CRYSTAL WAS TWINNED BY THE RETICULAR MEROHEDRY. THE DATA WERE DETWINNED USING THE ORIGINAL ALGORITHM AS DESCRIBED IN A SECONDARY REFERENCE
Crystal growDetails: 0.1M HEPES, 20% PEG6000 PH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.729
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.729 Å / Relative weight: 1
ReflectionResolution: 1.9→23.21 Å / Num. obs: 27770 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 3.48 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 16
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 5.7 / % possible all: 75

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Processing

Software
NameVersionClassification
REFMAC5.4.0057refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QQ5

1qq5


Resolution: 1.9→23.21 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.31 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.217 920 3.2 %RANDOM
Rwork0.163 ---
obs0.164 27770 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20.67 Å2
2---1.71 Å20 Å2
3---1.55 Å2
Refinement stepCycle: LAST / Resolution: 1.9→23.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3372 0 12 305 3689
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223556
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2661.9684805
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1845435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.10624.368174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63315687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4941520
X-RAY DIFFRACTIONr_chiral_restr0.090.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022664
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_it1.75432077
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.97753380
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.32871479
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.5881411
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: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 65 -
Rwork0.253 1514 -
obs--100 %

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