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- PDB-5e3b: Structure of macrodomain protein from Streptomyces coelicolor -

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Basic information

Entry
Database: PDB / ID: 5e3b
TitleStructure of macrodomain protein from Streptomyces coelicolor
ComponentsMacrodomain protein
KeywordsHYDROLASE / Macrodomain protein
Function / homology
Function and homology information


peptidyl-glutamate ADP-deribosylation
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-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsLalic, J. / Posavec Marjanovic, M. / Perina, D. / Sabljic, I. / Zaja, R. / Plese, B. / Imesek, M. / Bucca, G. / Ahel, M. / Cetkovic, H. ...Lalic, J. / Posavec Marjanovic, M. / Perina, D. / Sabljic, I. / Zaja, R. / Plese, B. / Imesek, M. / Bucca, G. / Ahel, M. / Cetkovic, H. / Luic, M. / Mikoc, A. / Ahel, I.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Disruption of Macrodomain Protein SCO6735 Increases Antibiotic Production in Streptomyces coelicolor.
Authors: Lalic, J. / Posavec Marjanovic, M. / Palazzo, L. / Perina, D. / Sabljic, I. / Zaja, R. / Colby, T. / Plese, B. / Halasz, M. / Jankevicius, G. / Bucca, G. / Ahel, M. / Matic, I. / Cetkovic, H. ...Authors: Lalic, J. / Posavec Marjanovic, M. / Palazzo, L. / Perina, D. / Sabljic, I. / Zaja, R. / Colby, T. / Plese, B. / Halasz, M. / Jankevicius, G. / Bucca, G. / Ahel, M. / Matic, I. / Cetkovic, H. / Luic, M. / Mikoc, A. / Ahel, I.
History
DepositionOct 2, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Jan 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Macrodomain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6734
Polymers19,5651
Non-polymers1083
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint-13 kcal/mol
Surface area7570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.819, 103.819, 33.254
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1252-

HOH

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Components

#1: Protein Macrodomain protein


Mass: 19565.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria)
Strain: ATCC BAA-471 / A3(2) / M145 / Gene: SCO6735 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X7P1
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.58 Å3/Da / Density % sol: 52.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Tris-HCl, 0.29 M sodium chloride, 1.0 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.6→46.43 Å / Num. obs: 24097 / % possible obs: 97.9 % / Redundancy: 8.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.043 / Net I/σ(I): 11.5 / Num. measured all: 206585
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.6-1.638.11.181.8861110570.670.43389.5
8.77-46.437.10.0692514342010.9960.02799.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.547
Highest resolutionLowest resolution
Rotation36.71 Å1.87 Å

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Processing

Software
NameVersionClassification
Aimless0.5.12data scaling
MOLREPphasing
REFMAC5.8.0124refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FG1

2fg1


Resolution: 1.6→46.43 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.2117 / WRfactor Rwork: 0.1754 / FOM work R set: 0.8435 / SU B: 1.766 / SU ML: 0.061 / SU R Cruickshank DPI: 0.0834 / SU Rfree: 0.0885 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2233 1196 5 %RANDOM
Rwork0.1842 ---
obs0.1861 22860 97.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.74 Å2 / Biso mean: 19.9 Å2 / Biso min: 9.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å2-0 Å2-0 Å2
2--0.41 Å2-0 Å2
3----0.82 Å2
Refinement stepCycle: final / Resolution: 1.6→46.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1128 0 6 161 1295
Biso mean--22.53 31.52 -
Num. residues----148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191205
X-RAY DIFFRACTIONr_bond_other_d0.0020.021139
X-RAY DIFFRACTIONr_angle_refined_deg2.2521.9251646
X-RAY DIFFRACTIONr_angle_other_deg1.17532594
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0815159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.12521.27355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.68415176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2521515
X-RAY DIFFRACTIONr_chiral_restr0.1420.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211403
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02306
X-RAY DIFFRACTIONr_mcbond_it2.4061.803609
X-RAY DIFFRACTIONr_mcbond_other2.4051.801608
X-RAY DIFFRACTIONr_mcangle_it3.2892.689762
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 59 -
Rwork0.263 1539 -
all-1598 -
obs--89.47 %

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