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- PDB-2x47: Crystal structure of human MACROD1 -

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Basic information

Entry
Database: PDB / ID: 2x47
TitleCrystal structure of human MACROD1
ComponentsMACRO DOMAIN-CONTAINING PROTEIN 1
KeywordsSIGNALING PROTEIN / SIGNAL TRANSDUCTION / ESTROGEN SIGNALING
Function / homology
Function and homology information


O-acetyl-ADP-ribose deacetylase / peptidyl-glutamate ADP-deribosylation / ADP-ribosylglutamate hydrolase activity / protein de-ADP-ribosylation / purine nucleoside metabolic process / O-acetyl-ADP-ribose deacetylase activity / deacetylase activity / hydrolase activity, acting on glycosyl bonds / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / DNA damage response ...O-acetyl-ADP-ribose deacetylase / peptidyl-glutamate ADP-deribosylation / ADP-ribosylglutamate hydrolase activity / protein de-ADP-ribosylation / purine nucleoside metabolic process / O-acetyl-ADP-ribose deacetylase activity / deacetylase activity / hydrolase activity, acting on glycosyl bonds / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / DNA damage response / mitochondrion / nucleoplasm / nucleus
Similarity search - Function
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
ADP-ribose glycohydrolase MACROD1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsVollmar, M. / Phillips, C. / Mehrotra, P.V. / Ahel, I. / Krojer, T. / Yue, W. / Ugochukwu, E. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. ...Vollmar, M. / Phillips, C. / Mehrotra, P.V. / Ahel, I. / Krojer, T. / Yue, W. / Ugochukwu, E. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Gileadi, O.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Identification of Macro Domain Proteins as Novel O-Acetyl-Adp-Ribose Deacetylases.
Authors: Chen, D. / Vollmar, M. / Rossi, M.N. / Phillips, C. / Kraehenbuehl, R. / Slade, D. / Mehrotra, P.V. / von Delft, F. / Crosthwaite, S.K. / Gileadi, O. / Denu, J.M. / Ahel, I.
History
DepositionJan 28, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Sep 21, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Structure summary
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Dec 20, 2023Group: 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: MACRO DOMAIN-CONTAINING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5533
Polymers26,3601
Non-polymers1922
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.920, 63.410, 75.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MACRO DOMAIN-CONTAINING PROTEIN 1 / HUMAN MACRO DOMAIN 1 / LRP16


Mass: 26360.488 Da / Num. of mol.: 1 / Fragment: MACRO DOMAIN, RESIDUES 91-325
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNH-TRXT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q9BQ69
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE STARTS WITH THR91 AS A RESULT OF CONSTRUCT DESIGN

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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: 1.86 Å3/Da / Density % sol: 33.94 % / Description: NONE
Crystal growDetails: 0.2M (NH4)2SO4, 0.1M HEPES PH 7.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→39.29 Å / Num. obs: 24711 / % possible obs: 98.7 % / Observed criterion σ(I): 2.8 / Redundancy: 3.5 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.9 / % possible all: 92.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0089refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SPV

1spv


Resolution: 1.7→75.9 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.187 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES RESIDUAL ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.20583 1251 5.1 %RANDOM
Rwork0.16452 ---
obs0.16652 23459 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.057 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.7→75.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1758 0 10 282 2050
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221802
X-RAY DIFFRACTIONr_bond_other_d0.0010.021222
X-RAY DIFFRACTIONr_angle_refined_deg1.561.9792439
X-RAY DIFFRACTIONr_angle_other_deg1.3332988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8765227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.80823.57170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.90315309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2791512
X-RAY DIFFRACTIONr_chiral_restr0.0950.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211979
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02356
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_it0.9011.51138
X-RAY DIFFRACTIONr_mcbond_other0.261.5463
X-RAY DIFFRACTIONr_mcangle_it1.5921821
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.463664
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8684.5618
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: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 81 -
Rwork0.265 1529 -
obs--89.15 %
Refinement TLS params.Method: refined / Origin x: 1.2124 Å / Origin y: 8.867 Å / Origin z: 15.3436 Å
111213212223313233
T0.0301 Å2-0.0008 Å2-0.0078 Å2-0.0054 Å20.0097 Å2--0.0244 Å2
L1.182 °2-0.0376 °2-0.3616 °2-0.8304 °2-0.0766 °2--1.1085 °2
S-0.0686 Å °0.0067 Å °-0.0424 Å °0.0105 Å °0.0053 Å °-0.018 Å °-0.0102 Å °0.0123 Å °0.0633 Å °

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