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- PDB-5fsu: Crystal structure of Trypanosoma brucei macrodomain (crystal form 1) -

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Basic information

Entry
Database: PDB / ID: 5fsu
TitleCrystal structure of Trypanosoma brucei macrodomain (crystal form 1)
ComponentsMACRODOMAIN
KeywordsHYDROLASE / MACRODOMAIN / ADP-RIBOSE BINDING
Function / homology
Function and homology information


Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / 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: 1.95 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 / 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

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Assembly

Deposited unit
A: MACRODOMAIN
B: MACRODOMAIN


Theoretical massNumber of molelcules
Total (without water)58,3512
Polymers58,3512
Non-polymers00
Water3,837213
1
A: MACRODOMAIN


Theoretical massNumber of molelcules
Total (without water)29,1761
Polymers29,1761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MACRODOMAIN


Theoretical massNumber of molelcules
Total (without water)29,1761
Polymers29,1761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.140, 77.140, 427.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein MACRODOMAIN


Mass: 29175.555 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 3.16 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growpH: 7.5
Details: 0.2 M SODIUM SULFATE, 0.1 M BIS-TRIS PROPANE PH 7.5, 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: 1.95→30 Å / Num. obs: 56483 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 15.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.9
Reflection shellResolution: 1.95→2 Å / Redundancy: 15.1 % / Mean I/σ(I) obs: 1.8 / % 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 4IQY

4iqy


Resolution: 1.95→19.75 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.992 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21912 2825 5 %RANDOM
Rwork0.18889 ---
obs0.19042 53658 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.727 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20.77 Å20 Å2
2--1.54 Å20 Å2
3----4.99 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3649 0 0 213 3862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193778
X-RAY DIFFRACTIONr_bond_other_d0.0010.023637
X-RAY DIFFRACTIONr_angle_refined_deg1.431.9835126
X-RAY DIFFRACTIONr_angle_other_deg0.91838373
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0355483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.71921.824159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70415631
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2741542
X-RAY DIFFRACTIONr_chiral_restr0.0830.2573
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214256
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02862
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_it2.945.0991914
X-RAY DIFFRACTIONr_mcbond_other2.9415.0971913
X-RAY DIFFRACTIONr_mcangle_it4.0687.6182391
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7715.6021864
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: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 203 -
Rwork0.402 3853 -
obs--99.68 %

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