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- PDB-2o2i: Crystal structure of haloalkane dehalogenase Rv2579 from Mycobact... -

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Basic information

Entry
Database: PDB / ID: 2o2i
TitleCrystal structure of haloalkane dehalogenase Rv2579 from Mycobacterium tuberculosis complexed with 1,3-propandiol
ComponentsHaloalkane dehalogenase 3
KeywordsHYDROLASE / haloalkane dehalogenase / Mycobacterium tuberculosis / Rv2579 / 1 / 3-propandiol / alpha/beta-hydrolase protein / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


halogenated hydrocarbon catabolic process / haloalkane dehalogenase / haloalkane dehalogenase activity / peptidoglycan-based cell wall / hydrolase activity / plasma membrane
Similarity search - Function
Haloalkane dehalogenase, subfamily 2 / 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
BROMIDE ION / 1,3-PROPANDIOL / Haloalkane dehalogenase 3 / Haloalkane dehalogenase 3
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMazumdar, P.A. / Hulecki, J. / Cherney, M.M. / Garen, C.R. / James, M.N.G. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: To be Published
Title: Crystal structure of haloalkane dehalogenase Rv2579 from Mycobacterium tuberculosis complexed with 1,3-propandiol
Authors: Mazumdar, P.A. / Hulecki, J. / Cherney, M.M. / Garen, C.R. / James, M.N.G.
History
DepositionNov 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Haloalkane dehalogenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9203
Polymers33,7641
Non-polymers1562
Water5,350297
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.820, 65.190, 126.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-310-

HOH

21A-318-

HOH

31A-425-

HOH

41A-549-

HOH

51A-550-

HOH

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Components

#1: Protein Haloalkane dehalogenase 3


Mass: 33764.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: dhaA / Plasmid: pDEST-15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: Q50642, UniProt: P9WMR9*PLUS, haloalkane dehalogenase
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 1.85 Å3/Da / Density % sol: 33.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 4000, 0.2M magnesium acetate, 0.1M Tris, 5% ethylene glycol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115879
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115879 Å / Relative weight: 1
ReflectionResolution: 1.5→63.043 Å / Num. all: 40063 / Num. obs: 39855 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 10.1 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 5.2
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 3.6 / Num. measured all: 15268 / Num. unique all: 5410 / Rsym value: 0.193 / % possible all: 92.9

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å63.04 Å
Translation2.5 Å63.04 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1MJ5

1mj5


Resolution: 1.5→36.35 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.11 / SU ML: 0.043 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.068 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.176 2003 5 %RANDOM
Rwork0.144 ---
obs0.146 39807 98.29 %-
all-39807 --
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: 9.054 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→36.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2312 0 6 297 2615
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222385
X-RAY DIFFRACTIONr_bond_other_d0.0020.021645
X-RAY DIFFRACTIONr_angle_refined_deg1.8431.9453245
X-RAY DIFFRACTIONr_angle_other_deg1.08633964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2665292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.48423.017116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.14415363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7091521
X-RAY DIFFRACTIONr_chiral_restr0.1360.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022692
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02516
X-RAY DIFFRACTIONr_nbd_refined0.2320.2502
X-RAY DIFFRACTIONr_nbd_other0.2160.21828
X-RAY DIFFRACTIONr_nbtor_refined0.190.21191
X-RAY DIFFRACTIONr_nbtor_other0.090.21236
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2184
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1330.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3780.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.236
X-RAY DIFFRACTIONr_mcbond_it1.3361.51557
X-RAY DIFFRACTIONr_mcbond_other0.3761.5590
X-RAY DIFFRACTIONr_mcangle_it1.72522349
X-RAY DIFFRACTIONr_scbond_it2.44531041
X-RAY DIFFRACTIONr_scangle_it3.5914.5896
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 151 -
Rwork0.162 2578 -
obs-2729 91.61 %

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