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- PDB-5fud: Oceanobacillus iheyensis macrodomain with MES bound -

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Basic information

Entry
Database: PDB / ID: 5fud
TitleOceanobacillus iheyensis macrodomain with MES bound
ComponentsO-ACETYL-ADP-RIBOSE DEACETYLASE
KeywordsHYDROLASE / BACTERIAL MACRODOMAIN / ADP-RIBOSE / DEACETYLASE
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
Hypothetical conserved protein
Similarity search - Component
Biological speciesOCEANOBACILLUS IHEYENSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 ofOceanobacillus iheyensismacrodomain 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
DepositionJan 25, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Nov 21, 2018Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / reflns / reflns_shell
Item: _citation.title / _citation_author.identifier_ORCID ..._citation.title / _citation_author.identifier_ORCID / _reflns.pdbx_Rsym_value / _reflns_shell.pdbx_Rsym_value
Revision 1.3Jan 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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

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Assembly

Deposited unit
A: O-ACETYL-ADP-RIBOSE DEACETYLASE
B: O-ACETYL-ADP-RIBOSE DEACETYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2227
Polymers45,6042
Non-polymers6185
Water3,927218
1
A: O-ACETYL-ADP-RIBOSE DEACETYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1294
Polymers22,8021
Non-polymers3273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: O-ACETYL-ADP-RIBOSE DEACETYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0933
Polymers22,8021
Non-polymers2912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.990, 96.740, 54.400
Angle α, β, γ (deg.)90.00, 115.65, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 6

Dom-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1PHEPHEAA-3 - 18520 - 208
2SERSERBB-4 - 18519 - 208

NCS oper:
IDCodeMatrixVector
1given(1, 0.003566, 0.000506), (0.003562, -1, 0.006486), (0.00053, -0.006484, -1)0.01553, -15.97, -17.59
2given(0.999998, 0.001565, 0.000979), (0.001558, -0.999975, 0.006909), (0.00099, -0.006908, -0.999976)0.00308, -15.93712, -17.60433

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Components

#1: Protein O-ACETYL-ADP-RIBOSE DEACETYLASE


Mass: 22801.857 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) OCEANOBACILLUS IHEYENSIS (bacteria) / Strain: HTE831 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2
References: UniProt: Q8EP31, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.74 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growpH: 6.5
Details: 0.2 M AMMONIUM SULPHATE, 0.1 M MES, PH 6.5, 30% (W/V) PEG [POLY(ETHYLENE GLYCOL)] MME 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97944
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2013 / Details: KB MIRRORS
RadiationMonochromator: CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97944 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.736
11-H, -K, H+L20.264
ReflectionResolution: 1.9→49 Å / Num. obs: 33155 / % possible obs: 96.3 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.1 / Rsym value: 0.098 / Net I/σ(I): 6.3
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.356 / % possible all: 93.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SPV

1spv


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.911 / SU B: 2.823 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2121 1666 5 %RANDOM
Rwork0.17097 ---
obs0.17304 31435 95.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.493 Å2
Baniso -1Baniso -2Baniso -3
1--2.24 Å20 Å2-1.31 Å2
2--13.03 Å20 Å2
3----10.79 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2899 0 35 218 3152
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022981
X-RAY DIFFRACTIONr_bond_other_d0.0010.021924
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.9734054
X-RAY DIFFRACTIONr_angle_other_deg0.91634761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.055377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.04725.969129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.0515498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.549158
X-RAY DIFFRACTIONr_chiral_restr0.080.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213293
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02535
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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: 1.898→1.946 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 118 -
Rwork0.199 2131 -
obs--87.51 %

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