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- PDB-5nyr: Anbu from Hyphomicrobium sp. strain MC1 -SG: R3 -

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Basic information

Entry
Database: PDB / ID: 5nyr
TitleAnbu from Hyphomicrobium sp. strain MC1 -SG: R3
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 / : / Peptidase
Function and homology information
Biological speciesHyphomicrobium sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 / 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

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Assembly

Deposited unit
A: Anbu
B: Anbu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4387
Polymers54,9582
Non-polymers4805
Water1,74797
1
B: Anbu
hetero molecules

A: Anbu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4387
Polymers54,9582
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_444-x+y-1/3,-x-2/3,z-2/31
2
A: Anbu
hetero molecules

B: Anbu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4387
Polymers54,9582
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_445-y-2/3,x-y-1/3,z+2/31
Buried area3920 Å2
ΔGint-92 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.490, 174.490, 39.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Anbu


Mass: 27478.965 Da / Num. of mol.: 2
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.1 Å3/Da / Density % sol: 41.39 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05 M ammonium sulfate, 0.05 M Bis-Tris, 30 % pentaerythritol propoxylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 29744 / % possible obs: 98.5 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.8
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2.5 / % 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: 2→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 10.973 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21367 1486 5 %RANDOM
Rwork0.18204 ---
obs0.1836 28233 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.642 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å2-0.55 Å20 Å2
2---1.1 Å20 Å2
3---3.57 Å2
Refinement stepCycle: 1 / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3323 0 25 97 3445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193402
X-RAY DIFFRACTIONr_bond_other_d0.0010.023149
X-RAY DIFFRACTIONr_angle_refined_deg0.9951.9574591
X-RAY DIFFRACTIONr_angle_other_deg0.81937248
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4395405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.99723.278180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.08115577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1791536
X-RAY DIFFRACTIONr_chiral_restr0.0570.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023770
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02762
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_it1.8135.3251644
X-RAY DIFFRACTIONr_mcbond_other1.8125.3211643
X-RAY DIFFRACTIONr_mcangle_it2.2847.9372041
X-RAY DIFFRACTIONr_mcangle_other2.2847.9422042
X-RAY DIFFRACTIONr_scbond_it1.8535.8721758
X-RAY DIFFRACTIONr_scbond_other1.8325.8551736
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.998.62520
X-RAY DIFFRACTIONr_long_range_B_refined3.06861.713546
X-RAY DIFFRACTIONr_long_range_B_other2.95961.6643541
X-RAY DIFFRACTIONr_rigid_bond_restr0.73436551
X-RAY DIFFRACTIONr_sphericity_free31.143559
X-RAY DIFFRACTIONr_sphericity_bonded11.39356535
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 109 -
Rwork0.295 2068 -
obs--99.82 %
Refinement TLS params.

T13: -0.0023 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.20930.0872-0.01820.45740.00820.0124-0.01820.009-0.0534-0.02350.02250.0317-0.01830-0.00430.0438-0.00020.03980.00020.0422-27.8944-21.4584-16.8133
20.5110.1699-0.06390.34210.06950.04860.0147-0.0221-0.05040.03-0.01990.0269-0.00070.02010.00530.0426-0.00010.04310.00310.0373-1.6956-29.944-35.388
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 242
2X-RAY DIFFRACTION2B1 - 240

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