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- PDB-3p2m: Crystal Structure of a Novel Esterase Rv0045c from Mycobacterium ... -

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Basic information

Entry
Database: PDB / ID: 3p2m
TitleCrystal Structure of a Novel Esterase Rv0045c from Mycobacterium tuberculosis
ComponentsPOSSIBLE HYDROLASE
KeywordsHYDROLASE / Alpha/beta hydrolase superfamily
Function / homology
Function and homology information


carboxylesterase activity
Similarity search - Function
: / Alpha/beta hydrolase family / 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
AB hydrolase-1 domain-containing protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsZheng, X.D. / Guo, J. / Xu, L. / Li, H. / Zhang, D. / Zhang, K. / Sun, F. / Wen, T. / Liu, S. / Pang, H.
CitationJournal: Plos One / Year: 2011
Title: Crystal Structure of a Novel Esterase Rv0045c from Mycobacterium tuberculosis
Authors: Zheng, X.D. / Guo, J. / Xu, L. / Li, H. / Zhang, D. / Zhang, K. / Sun, F. / Wen, T. / Liu, S. / Pang, H.
History
DepositionOct 3, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: POSSIBLE HYDROLASE


Theoretical massNumber of molelcules
Total (without water)35,5451
Polymers35,5451
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.465, 73.465, 48.063
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein POSSIBLE HYDROLASE / hydrolase Rv0045c / Putative uncharacterized protein


Mass: 35544.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv0045c / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P71702, Hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.09 Å3/Da / Density % sol: 41.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M magnesium chloride, 100 mM Tris-HCl, 30% PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.07176 / Wavelength: 1.07176 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07176 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 7159 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 80.8 Å2 / Rsym value: 0.079 / Net I/σ(I): 26.5
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 3 / Rsym value: 0.397 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→38.35 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.882 / SU B: 20.082 / SU ML: 0.396 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.46
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.286 336 4.7 %RANDOM
Rwork0.217 ---
obs0.22 6810 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20.5 Å20 Å2
2--0.99 Å20 Å2
3----1.49 Å2
Refinement stepCycle: LAST / Resolution: 2.8→38.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2136 0 0 36 2172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212183
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.571.9442973
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1395279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.80523.107103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.28715328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.411521
X-RAY DIFFRACTIONr_chiral_restr0.0980.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211701
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_it0.7261.51388
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35922213
X-RAY DIFFRACTIONr_scbond_it1.5433795
X-RAY DIFFRACTIONr_scangle_it2.744.5760
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.88 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 18 -
Rwork0.265 522 -
obs--99.82 %

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