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- PDB-2yml: Native L-haloacid dehalogenase from a Rhodobacteraceae family bac... -

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Basic information

Entry
Database: PDB / ID: 2yml
TitleNative L-haloacid dehalogenase from a Rhodobacteraceae family bacterium
ComponentsL-HALOACID DEHALOGENASE
KeywordsHYDROLASE
Function / homology
Function and homology information


(S)-2-haloacid dehalogenase / (S)-2-haloacid dehalogenase activity
Similarity search - Function
L-2-Haloacid dehalogenase / : / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 ...L-2-Haloacid dehalogenase / : / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / 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
(S)-2-haloacid dehalogenase
Similarity search - Component
Biological speciesRHODOBACTERACEAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsNovak, H.R. / Sayer, C. / Isupov, M.N. / Paszkiewicz, K. / Gotz, D. / Spragg, A.M. / Littlechild, J.A.
CitationJournal: FEBS J. / Year: 2013
Title: Marine Rhodobacteraceae L-Haloacid Dehalogenase Contains a Novel His/Glu Dyad that Could Activate the Catalytic Water.
Authors: Novak, H.R. / Sayer, C. / Isupov, M.N. / Paszkiewicz, K. / Gotz, D. / Mearns Spragg, A. / Littlechild, J.A.
History
DepositionOct 9, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-HALOACID DEHALOGENASE
B: L-HALOACID DEHALOGENASE


Theoretical massNumber of molelcules
Total (without water)51,4932
Polymers51,4932
Non-polymers00
Water11,620645
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-33.8 kcal/mol
Surface area17370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.840, 68.340, 159.730
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: (-0.99986, -0.00994, 0.01334), (-0.01637, 0.72981, -0.68345), (-0.00295, -0.68358, -0.72987)
Vector: 68.24697, 49.33384, 123.43266)

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Components

#1: Protein L-HALOACID DEHALOGENASE


Mass: 25746.334 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOBACTERACEAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIPL / References: UniProt: R4GRT2*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 645 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE MATCHES TO GENBANK JX868516

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 45.4 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.92
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.79→39.93 Å / Num. obs: 46369 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.1
Reflection shellResolution: 1.79→1.83 Å / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NO4

2no4


Resolution: 1.79→39.93 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.547 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20408 2347 5.1 %RANDOM
Rwork0.15747 ---
obs0.15981 44022 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 mean: 22.925 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20 Å2
2--0.5 Å20 Å2
3----1.15 Å2
Refinement stepCycle: LAST / Resolution: 1.79→39.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3480 0 0 645 4125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193834
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.9765297
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5465531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.55523.374163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.45415637
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7491529
X-RAY DIFFRACTIONr_chiral_restr0.0980.2615
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212969
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: 1.787→1.833 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 155 -
Rwork0.239 3238 -
obs--99.76 %

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