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- PDB-2no5: Crystal Structure analysis of a Dehalogenase with intermediate complex -

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Basic information

Entry
Database: PDB / ID: 2no5
TitleCrystal Structure analysis of a Dehalogenase with intermediate complex
Components(S)-2-haloacid dehalogenase IVA
KeywordsHYDROLASE / Haloacid dehalogenase / Dehalogenase / HAD Superfamily / Intermediate structure
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 / Rossmann fold ...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
(2S)-2-CHLOROPROPANOIC ACID / (S)-2-haloacid dehalogenase 4A
Similarity search - Component
Biological speciesBurkholderia cepacia (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsSchmidberger, J.W. / Wilce, M.C.J.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal structures of the substrate free-enzyme, and reaction intermediate of the HAD superfamily member, haloacid dehalogenase DehIVa from Burkholderia cepacia MBA4
Authors: Schmidberger, J.W. / Wilce, J.A. / Tsang, J.S.H. / Wilce, M.C.J.
History
DepositionOct 24, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: (S)-2-haloacid dehalogenase IVA
B: (S)-2-haloacid dehalogenase IVA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,02319
Polymers54,4132
Non-polymers1,61017
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-228 kcal/mol
Surface area18130 Å2
MethodPISA
2
A: (S)-2-haloacid dehalogenase IVA
B: (S)-2-haloacid dehalogenase IVA
hetero molecules

A: (S)-2-haloacid dehalogenase IVA
B: (S)-2-haloacid dehalogenase IVA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,04738
Polymers108,8274
Non-polymers3,22034
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
MethodPQS
Unit cell
Length a, b, c (Å)103.743, 103.743, 134.794
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-1022-

HOH

DetailsThe structure is a Functional homodimer in the ASU. Asp11 on each chain (A and B) is covalently bound to a reaction intermediate, of the substrate L-2-monochloroprapanate.

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Components

#1: Protein (S)-2-haloacid dehalogenase IVA / Dehalogenase / 2-haloalkanoic acid dehalogenase IVA / L-2-haloacid dehalogenase IVA / ...Dehalogenase / 2-haloalkanoic acid dehalogenase IVA / L-2-haloacid dehalogenase IVA / Halocarboxylic acid halidohydrolase IVA


Mass: 27206.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cepacia (bacteria) / Strain: MBA4 / Plasmid: pHKU201 / Production host: Escherichia coli (E. coli) / References: UniProt: Q51645, (S)-2-haloacid dehalogenase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CNR / (2S)-2-CHLOROPROPANOIC ACID / 2-MONOCHLOROPRAPANATE


Mass: 108.524 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5ClO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 4.01 Å3/Da / Density % sol: 69.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 20% PEG 4000, 0.65M Ammonium Sulphate, pH 4.8, 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: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 16, 2004 / Details: Osmic mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→29.24 Å / Num. all: 26826 / Num. obs: 26322 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Redundancy: 3.49 % / Biso Wilson estimate: 55.1 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 10.13
Reflection shellResolution: 2.58→2.67 Å / Redundancy: 3.11 % / Mean I/σ(I) obs: 1.41 / Num. unique all: 1919 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345dtbdata collection
MOSFLMdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2NO4

2no4


Resolution: 2.6→29.24 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.899 / SU B: 8.856 / SU ML: 0.189 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.324 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1315 5 %RANDOM
Rwork0.196 ---
obs0.199 25671 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.139 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3592 0 84 89 3765
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223791
X-RAY DIFFRACTIONr_angle_refined_deg1.8451.9845148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0575450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.66424.153183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.26115639
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9181526
X-RAY DIFFRACTIONr_chiral_restr0.1240.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022864
X-RAY DIFFRACTIONr_nbd_refined0.2430.21855
X-RAY DIFFRACTIONr_nbtor_refined0.3220.22553
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2191
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2590.29
X-RAY DIFFRACTIONr_mcbond_it1.85922303
X-RAY DIFFRACTIONr_mcangle_it3.01133622
X-RAY DIFFRACTIONr_scbond_it1.81721683
X-RAY DIFFRACTIONr_scangle_it2.74131525
LS refinement shellResolution: 2.599→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 82 -
Rwork0.265 1837 -
obs-1919 100 %

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