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- PDB-5lcc: Oceanobacillus iheyensis macrodomain mutant D40A -

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Basic information

Entry
Database: PDB / ID: 5lcc
TitleOceanobacillus iheyensis macrodomain mutant D40A
ComponentsMACROD-TYPE MACRODOMAIN
KeywordsHYDROLASE / macrodomain / ADP-ribosylation / deacetylase
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
Hypothetical conserved protein
Similarity search - Component
Biological speciesOceanobacillus iheyensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGil-Ortiz, F. / Zapata-Perez, R. / Martinez, A.B. / Juanhuix, J. / Sanchez-Ferrer, A.
CitationJournal: Open Biol / Year: 2017
Title: Structural and functional analysis of Oceanobacillus iheyensis macrodomain reveals a network of waters involved in substrate binding and catalysis.
Authors: Zapata-Perez, R. / Gil-Ortiz, F. / Martinez-Monino, A.B. / Garcia-Saura, A.G. / Juanhuix, J. / Sanchez-Ferrer, A.
History
DepositionJun 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MACROD-TYPE MACRODOMAIN
B: MACROD-TYPE MACRODOMAIN


Theoretical massNumber of molelcules
Total (without water)45,5042
Polymers45,5042
Non-polymers00
Water2,738152
1
A: MACROD-TYPE MACRODOMAIN


Theoretical massNumber of molelcules
Total (without water)22,7521
Polymers22,7521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MACROD-TYPE MACRODOMAIN


Theoretical massNumber of molelcules
Total (without water)22,7521
Polymers22,7521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.716, 63.245, 120.365
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A1 - 500
2116B1 - 500

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.634474, 0.718625, -0.284642), (0.741081, -0.460926, 0.488207), (0.219639, -0.520697, -0.825005)17.82845, 8.67876, 20.50243

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Components

#1: Protein MACROD-TYPE MACRODOMAIN


Mass: 22751.889 Da / Num. of mol.: 2 / Mutation: D40A
Source method: isolated from a genetically manipulated source
Details: Engineered mutant D40A
Source: (gene. exp.) Oceanobacillus iheyensis (strain DSM 14371 / JCM 11309 / KCTC 3954 / HTE831) (bacteria)
Strain: DSM 14371 / JCM 11309 / KCTC 3954 / HTE831 / Gene: OB2288 / Plasmid: pET28-MacroD / Production host: Escherichia coli (E. coli) / Variant (production host): Rossetta 2 / References: UniProt: Q8EP31
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M magnesium formate, 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2015 / Details: KB mirrors
RadiationMonochromator: Channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→15 Å / Num. obs: 25874 / % possible obs: 90.8 % / Redundancy: 5.1 % / Biso Wilson estimate: 32.39 Å2 / CC1/2: 0.999 / Rsym value: 0.045 / Net I/σ(I): 18.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 3.9 / % possible all: 90.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1spv

1spv


Resolution: 2→15 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.629 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.173 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23134 1253 4.9 %RANDOM
Rwork0.18498 ---
obs0.18718 24291 89.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.243 Å2
Baniso -1Baniso -2Baniso -3
1-2.23 Å20 Å20 Å2
2--1.59 Å2-0 Å2
3----3.83 Å2
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2882 0 0 152 3034
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192942
X-RAY DIFFRACTIONr_bond_other_d0.0020.022866
X-RAY DIFFRACTIONr_angle_refined_deg1.4241.9664002
X-RAY DIFFRACTIONr_angle_other_deg0.96636593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7035379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24726.063127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.75715506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.457158
X-RAY DIFFRACTIONr_chiral_restr0.0870.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023363
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02629
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_it2.3733.991510
X-RAY DIFFRACTIONr_mcbond_other2.373.9881509
X-RAY DIFFRACTIONr_mcangle_it3.4465.9681885
X-RAY DIFFRACTIONr_mcangle_other3.4465.9711886
X-RAY DIFFRACTIONr_scbond_it3.2684.491432
X-RAY DIFFRACTIONr_scbond_other3.2674.4921433
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1586.5542116
X-RAY DIFFRACTIONr_long_range_B_refined6.69832.5063301
X-RAY DIFFRACTIONr_long_range_B_other6.66732.3233241
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2799 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Aloose positional0.685
Bloose thermal3.910
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 99 -
Rwork0.238 1937 -
obs--99.9 %

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