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- PDB-5ovu: Cupriavidus metallidurans BPH -

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Basic information

Entry
Database: PDB / ID: 5ovu
TitleCupriavidus metallidurans BPH
ComponentsBETA-PROTEOBACTERIA PROTEASOME HOMOLOGUE
KeywordsHYDROLASE / Protein Degradation / beta-proteobacteria proteasome homologue
Function / homologyproteasome core complex / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / : / MALONATE ION / 20S proteasome, A and B subunits
Function and homology information
Biological speciesCupriavidus metallidurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFuchs, A.C.D. / Albrecht, R. / Martin, J. / Hartmann, M.D.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural characterization of the bacterial proteasome homolog BPH reveals a tetradecameric double-ring complex with unique inner cavity properties.
Authors: Fuchs, A.C.D. / Maldoner, L. / Hipp, K. / Hartmann, M.D. / Martin, J.
History
DepositionAug 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
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 / struct_ncs_dom_lim
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-PROTEOBACTERIA PROTEASOME HOMOLOGUE
B: BETA-PROTEOBACTERIA PROTEASOME HOMOLOGUE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6776
Polymers43,2692
Non-polymers4084
Water2,288127
1
A: BETA-PROTEOBACTERIA PROTEASOME HOMOLOGUE
B: BETA-PROTEOBACTERIA PROTEASOME HOMOLOGUE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)262,06136
Polymers259,61212
Non-polymers2,44924
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area46650 Å2
ΔGint-117 kcal/mol
Surface area75670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.496, 96.496, 75.894
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 1 - 188 / Label seq-ID: 1 - 188

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein BETA-PROTEOBACTERIA PROTEASOME HOMOLOGUE / BPH


Mass: 21634.295 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus metallidurans (bacteria) / Gene: Rmet_1198 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1LP42
#2: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.29 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 100 mM sodium acetate pH 4.4, 1.5 M sodium nitrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→37.9 Å / Num. obs: 23627 / % possible obs: 99.8 % / Redundancy: 9.39 % / CC1/2: 0.997 / Rmerge(I) obs: 0.144 / Net I/σ(I): 11.7
Reflection shellResolution: 2.1→2.22 Å / Redundancy: 9.33 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 3757 / CC1/2: 0.796 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OVS

5ovs


Resolution: 2.1→37.9 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.911 / SU B: 16.03 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.273 / ESU R Free: 0.198 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25227 1182 5 %RANDOM
Rwork0.23693 ---
obs0.2377 22444 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.597 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å2-0.56 Å2-0 Å2
2---1.13 Å2-0 Å2
3---3.66 Å2
Refinement stepCycle: 1 / Resolution: 2.1→37.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2859 0 28 127 3014
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0192942
X-RAY DIFFRACTIONr_bond_other_d0.0010.022746
X-RAY DIFFRACTIONr_angle_refined_deg0.9191.953972
X-RAY DIFFRACTIONr_angle_other_deg0.70636287
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3835369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.46722.95139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5115472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.6771526
X-RAY DIFFRACTIONr_chiral_restr0.0520.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023372
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02702
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_it0.4142.3781482
X-RAY DIFFRACTIONr_mcbond_other0.4142.3771481
X-RAY DIFFRACTIONr_mcangle_it0.7333.5611846
X-RAY DIFFRACTIONr_mcangle_other0.7333.5611847
X-RAY DIFFRACTIONr_scbond_it0.432.4811460
X-RAY DIFFRACTIONr_scbond_other0.4282.4791458
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.7373.6882125
X-RAY DIFFRACTIONr_long_range_B_refined2.91618.7873130
X-RAY DIFFRACTIONr_long_range_B_other2.87418.6383107
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 10811 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.097→2.152 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 74 -
Rwork0.348 1636 -
obs--98.39 %
Refinement TLS params.

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)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5358-0.0140.54611.13950.50881.53370.0267-0.2136-0.11950.1305-0.0147-0.03780.1198-0.0066-0.01210.0366-0.00480.0370.03560.01460.1039-18.3542-25.48-0.1972
21.219-0.0101-0.34711.4426-0.57781.732-0.02180.22530.0302-0.20250.06120.11190.0182-0.1236-0.03940.0326-0.0091-0.02220.0641-0.03580.1209-25.3237-18.6757-34.6771
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 188
2X-RAY DIFFRACTION2B1 - 188

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