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- PDB-5fsx: Crystal structure of Trypanosoma brucei macrodomain in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5fsx
TitleCrystal structure of Trypanosoma brucei macrodomain in complex with ADP
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
ADENOSINE-5'-DIPHOSPHATE / Macro domain-containing protein
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI (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 2.0Oct 23, 2019Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
Revision 2.1Jan 10, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: MACRODOMAIN
B: MACRODOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2985
Polymers58,3512
Non-polymers9463
Water1,44180
1
A: MACRODOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6032
Polymers29,1761
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MACRODOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6953
Polymers29,1761
Non-polymers5192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.957, 115.590, 70.440
Angle α, β, γ (deg.)90.00, 93.81, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-2006-

HOH

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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: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.31 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 8
Details: 0.1 M MIB (MALONIC ACID, IMIDAZOLE, BORIC ACID) PH 8.0, 25 % W/V PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS3 6M / 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: 2→30 Å / Num. obs: 34730 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 39.67 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.14 / Mean I/σ(I) obs: 1.6 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FSU

5fsu


Resolution: 2→19.433 Å / SU ML: 0.31 / σ(F): 1.53 / Phase error: 35.84 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED TO RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.253 1745 5 %
Rwork0.2136 --
obs0.2156 34678 97.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→19.433 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3563 0 60 80 3703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083714
X-RAY DIFFRACTIONf_angle_d1.1615045
X-RAY DIFFRACTIONf_dihedral_angle_d14.0221388
X-RAY DIFFRACTIONf_chiral_restr0.041565
X-RAY DIFFRACTIONf_plane_restr0.006644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05880.43841330.39262705X-RAY DIFFRACTION96
2.0588-2.12520.47481500.35812702X-RAY DIFFRACTION97
2.1252-2.2010.32631500.33332705X-RAY DIFFRACTION97
2.201-2.2890.35781500.31272723X-RAY DIFFRACTION97
2.289-2.3930.34781380.30312716X-RAY DIFFRACTION97
2.393-2.51890.31361500.27272734X-RAY DIFFRACTION98
2.5189-2.67640.33051440.26142751X-RAY DIFFRACTION98
2.6764-2.88240.31241480.24742767X-RAY DIFFRACTION98
2.8824-3.17130.3031380.2412772X-RAY DIFFRACTION98
3.1713-3.62770.24531480.1972766X-RAY DIFFRACTION98
3.6277-4.56070.18331380.16862787X-RAY DIFFRACTION98
4.5607-19.43360.18131580.15192805X-RAY DIFFRACTION98

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