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- PDB-5fsv: Crystal structure of Trypanosoma brucei macrodomain (crystal form 2) -

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Basic information

Entry
Database: PDB / ID: 5fsv
TitleCrystal structure of Trypanosoma brucei macrodomain (crystal form 2)
ComponentsMACRODOMAIN
KeywordsHYDROLASE / MACRODOMAIN / ADP-RIBOSE BINDING
Function / homology
Function and homology information


Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Macro domain-containing protein
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsHaikarainen, T. / Lehtio, L.
CitationJournal: Sci.Rep. / Year: 2016
Title: Proximal Adp-Ribose Hydrolysis in Trypanosomatids is Catalyzed by a Macrodomain.
Authors: Haikarainen, T. / Lehtio, L.
History
DepositionJan 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: MACRODOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3603
Polymers29,1761
Non-polymers1842
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.390, 54.540, 58.820
Angle α, β, γ (deg.)90.00, 95.83, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MACRODOMAIN


Mass: 29175.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C9ZP98
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.16 Å3/Da / Density % sol: 43 % / Description: NONE
Crystal growpH: 8.5
Details: 0.2 M SODIUM FLUORIDE, 0.1 M BIS-TRIS PROPANE PH 8.5, 20 % W/V PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: May 3, 2015 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. obs: 76636 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 11.9
Reflection shellResolution: 1.2→1.23 Å / Redundancy: 3 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 1.5 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FSU

5fsu


Resolution: 1.2→19.51 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.98 / SU B: 1.552 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.15993 3832 5 %RANDOM
Rwork0.14385 ---
obs0.14465 72804 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.471 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å2-1.07 Å2
2---0.36 Å20 Å2
3---1.17 Å2
Refinement stepCycle: LAST / Resolution: 1.2→19.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1780 0 12 238 2030
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191960
X-RAY DIFFRACTIONr_bond_other_d0.0020.021918
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.992675
X-RAY DIFFRACTIONr_angle_other_deg0.95234438
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4635267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.9821.46382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.61215346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1881524
X-RAY DIFFRACTIONr_chiral_restr0.0910.2301
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212225
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02451
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_it1.3511.654974
X-RAY DIFFRACTIONr_mcbond_other1.3481.65973
X-RAY DIFFRACTIONr_mcangle_it1.8312.4881226
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1631.97986
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_restr1.74733877
X-RAY DIFFRACTIONr_sphericity_free33.399575
X-RAY DIFFRACTIONr_sphericity_bonded12.99453988
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 281 -
Rwork0.405 5351 -
obs--99.59 %

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