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- PDB-5fsz: Crystal structure of Trypanosoma cruzi macrodomain -

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Basic information

Entry
Database: PDB / ID: 5fsz
TitleCrystal structure of Trypanosoma cruzi macrodomain
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 CRUZI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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 1.1Sep 13, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.2Jan 10, 2024Group: 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: MACRODOMAIN


Theoretical massNumber of molelcules
Total (without water)29,4731
Polymers29,4731
Non-polymers00
Water1,13563
1
A: MACRODOMAIN

A: MACRODOMAIN


Theoretical massNumber of molelcules
Total (without water)58,9452
Polymers58,9452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area5310 Å2
ΔGint-28.8 kcal/mol
Surface area21780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.820, 74.820, 75.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein MACRODOMAIN


Mass: 29472.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA CRUZI (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4DQ03
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 1.8 Å3/Da / Density % sol: 32 % / Description: NONE
Crystal growpH: 8
Details: 0.1 M BIS-TRIS PROPANE PH 8.0, 0.96 M TRISODIUM CITRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 1, 2015
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 15003 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 11.1 % / Mean I/σ(I) obs: 1.5 / % possible all: 100

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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: 2→18.86 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.455 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25796 751 5 %RANDOM
Rwork0.18803 ---
obs0.19155 14251 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.095 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2--0.09 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 2→18.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1909 0 0 63 1972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191974
X-RAY DIFFRACTIONr_bond_other_d0.0020.021876
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.962684
X-RAY DIFFRACTIONr_angle_other_deg0.93934307
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1055248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.75221.72487
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5115317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5471520
X-RAY DIFFRACTIONr_chiral_restr0.0840.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212228
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02476
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_it2.5594.037983
X-RAY DIFFRACTIONr_mcbond_other2.5464.035982
X-RAY DIFFRACTIONr_mcangle_it3.7086.0421228
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.174.535991
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: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 54 -
Rwork0.302 1014 -
obs--100 %

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