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- PDB-2w43: Structure of L-haloacid dehalogenase from S. tokodaii -

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Basic information

Entry
Database: PDB / ID: 2w43
TitleStructure of L-haloacid dehalogenase from S. tokodaii
ComponentsHYPOTHETICAL 2-HALOALKANOIC ACID DEHALOGENASE
KeywordsHYDROLASE / METABOLIC PROCESS
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
PHOSPHATE ION / L-2-haloacid dehalogenase
Similarity search - Component
Biological speciesSULFOLOBUS TOKODAII (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsRye, C.A. / Isupov, M.N. / Lebedev, A.A. / Littlechild, J.A.
CitationJournal: 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.
History
DepositionNov 21, 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 1.3May 30, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.4Dec 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

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Assembly

Deposited unit
A: HYPOTHETICAL 2-HALOALKANOIC ACID DEHALOGENASE
B: HYPOTHETICAL 2-HALOALKANOIC ACID DEHALOGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6628
Polymers46,8922
Non-polymers7706
Water11,458636
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-25.7 kcal/mol
Surface area21170 Å2
MethodPQS
Unit cell
Length a, b, c (Å)69.796, 71.889, 85.601
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.92, -0.234, 0.315), (-0.242, -0.97, -0.012), (0.309, -0.066, -0.949)
Vector: 1.2201, 5.56395, -4.85091)

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Components

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


Mass: 23446.014 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, EC: 3.1.8.2
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 636 / 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: 2.24 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growDetails: 0.1M MES, 20% PEG6000, PH6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS / Wavelength: 1.54
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 21, 2006 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.66→15 Å / Num. obs: 51594 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 28.8
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 7.3 / % possible all: 99.8

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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: 1.66→55.05 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.792 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1062 2.1 %RANDOM
Rwork0.177 ---
obs0.178 50464 99.3 %-
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: 22.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2---1.03 Å20 Å2
3---1.48 Å2
Refinement stepCycle: LAST / Resolution: 1.66→55.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3306 0 44 636 3986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223626
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.9814926
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8195457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2624.318176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47515713
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4681522
X-RAY DIFFRACTIONr_chiral_restr0.0910.2535
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022706
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_it1.59732090
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.65253423
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.81371536
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.55681474
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: 1.66→1.7 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.403 74
Rwork0.334 3619

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