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- PDB-5nyp: Anbu from Hyphomicrobium sp. strain MC1 - SG: R32 -

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Basic information

Entry
Database: PDB / ID: 5nyp
TitleAnbu from Hyphomicrobium sp. strain MC1 - SG: R32
ComponentsAnbu
KeywordsHYDROLASE / Ntn-hydrolase-fold / proteasome / evolution
Function / homologyUncharacterised conserved protein UCP009120, proteasome-type protease, Sll0069 / proteasome core complex / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / proteolysis involved in protein catabolic process / PHOSPHATE ION / Peptidase
Function and homology information
Biological speciesHyphomicrobium sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsVielberg, M.-T. / Groll, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB1035 Germany
CitationJournal: J. Mol. Biol. / Year: 2018
Title: On the Trails of the Proteasome Fold: Structural and Functional Analysis of the Ancestral beta-Subunit Protein Anbu.
Authors: Vielberg, M.T. / Bauer, V.C. / Groll, M.
History
DepositionMay 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _pdbx_audit_support.funding_organization
Revision 1.2Mar 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anbu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6924
Polymers27,4791
Non-polymers2133
Water1,00956
1
A: Anbu
hetero molecules

A: Anbu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3848
Polymers54,9582
Non-polymers4266
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_547y+1/3,x-1/3,-z+8/31
Buried area3820 Å2
ΔGint-33 kcal/mol
Surface area19630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.217, 176.217, 39.551
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-301-

NA

21A-303-

PO4

31A-454-

HOH

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Components

#1: Protein Anbu


Mass: 27478.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hyphomicrobium sp. (strain MC1) (bacteria)
Gene: HYPMC_4374 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F8JB59
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.43 Å3/Da / Density % sol: 49.42 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris, 2.0 M ammonium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 18422 / % possible obs: 99.6 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 17
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 2.7 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NYF

5nyf


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.954 / SU B: 7.723 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.422 / ESU R Free: 0.133 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2152 921 5 %RANDOM
Rwork0.18961 ---
obs0.1909 17483 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.786 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20.13 Å20 Å2
2--0.26 Å20 Å2
3----0.83 Å2
Refinement stepCycle: 1 / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1717 0 11 56 1784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191766
X-RAY DIFFRACTIONr_bond_other_d0.0010.021638
X-RAY DIFFRACTIONr_angle_refined_deg1.0281.9542385
X-RAY DIFFRACTIONr_angle_other_deg0.83133767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.265211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.50923.08594
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.62815298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8361519
X-RAY DIFFRACTIONr_chiral_restr0.0620.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021967
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02404
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_it1.2783.406850
X-RAY DIFFRACTIONr_mcbond_other1.2783.404849
X-RAY DIFFRACTIONr_mcangle_it1.6515.0891056
X-RAY DIFFRACTIONr_mcangle_other1.655.0911057
X-RAY DIFFRACTIONr_scbond_it1.063.701914
X-RAY DIFFRACTIONr_scbond_other1.0443.679906
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2715.4411315
X-RAY DIFFRACTIONr_long_range_B_refined2.25939.1351861
X-RAY DIFFRACTIONr_long_range_B_other2.1239.0241856
X-RAY DIFFRACTIONr_rigid_bond_restr0.6433400
X-RAY DIFFRACTIONr_sphericity_free29.478530
X-RAY DIFFRACTIONr_sphericity_bonded5.39353400
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 67 -
Rwork0.373 1272 -
obs--99.78 %
Refinement TLS params.Method: refined / Origin x: 118.28 Å / Origin y: 138.1349 Å / Origin z: 48.6974 Å
111213212223313233
T0.0303 Å2-0.0311 Å2-0.0051 Å2-0.0481 Å20.0021 Å2--0.0173 Å2
L2.8921 °20.7745 °20.5481 °2-0.6651 °20.1511 °2--0.5399 °2
S-0.0004 Å °0.2055 Å °-0.088 Å °0.0001 Å °0.0347 Å °-0.1025 Å °0.1125 Å °-0.0803 Å °-0.0343 Å °

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