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- PDB-5loy: Helical Assembly of a Designed Anbu Protein -

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Basic information

Entry
Database: PDB / ID: 5loy
TitleHelical Assembly of a Designed Anbu Protein
ComponentsDesigned Anbu Protein
KeywordsHYDROLASE / Protein Degradation / Ancestral Beta Subunit / Proteasome Precursor / Consensus Design / METAL BINDING PROTEIN
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFuchs, A.C.D. / Albrecht, R. / Martin, J. / Hartmann, M.D.
CitationJournal: Structure / Year: 2017
Title: The Architecture of the Anbu Complex Reflects an Evolutionary Intermediate at the Origin of the Proteasome System.
Authors: Fuchs, A.C.D. / Alva, V. / Maldoner, L. / Albrecht, R. / Hartmann, M.D. / Martin, J.
History
DepositionAug 10, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
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 / 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: Designed Anbu Protein
B: Designed Anbu Protein
C: Designed Anbu Protein
D: Designed Anbu Protein


Theoretical massNumber of molelcules
Total (without water)106,9774
Polymers106,9774
Non-polymers00
Water6,684371
1
A: Designed Anbu Protein
C: Designed Anbu Protein


Theoretical massNumber of molelcules
Total (without water)53,4892
Polymers53,4892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-26 kcal/mol
Surface area20330 Å2
MethodPISA
2
B: Designed Anbu Protein
D: Designed Anbu Protein


Theoretical massNumber of molelcules
Total (without water)53,4892
Polymers53,4892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-27 kcal/mol
Surface area20120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.742, 170.742, 92.127
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: TRP / End label comp-ID: TRP / Refine code: _ / Auth seq-ID: 1 - 239 / Label seq-ID: 1 - 239

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Designed Anbu Protein / ANCESTRAL BETA SUBUNIT


Mass: 26744.281 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Manually created consensus sequence based on a multiple sequence alignment of Anbu proteins
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 3.14 Å3/Da / Density % sol: 60.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES-NaOH pH 7.0, 0.6 M NaF

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→38.7 Å / Num. obs: 47607 / % possible obs: 99.8 % / Redundancy: 10.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.117 / Net I/σ(I): 18.96
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.991 / Mean I/σ(I) obs: 2.5 / CC1/2: 0.789 / % possible all: 98.9

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Processing

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

5lox


Resolution: 2.5→38.7 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.928 / SU B: 15.083 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.324 / ESU R Free: 0.23 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22237 2381 5 %RANDOM
Rwork0.18107 ---
obs0.1831 45226 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 47.019 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å2-0 Å20 Å2
2--0.61 Å20 Å2
3----1.22 Å2
Refinement stepCycle: 1 / Resolution: 2.5→38.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7133 0 0 371 7504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0197281
X-RAY DIFFRACTIONr_bond_other_d0.0050.026939
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.9819892
X-RAY DIFFRACTIONr_angle_other_deg0.995315924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0225908
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.72723.075335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.738151183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6851572
X-RAY DIFFRACTIONr_chiral_restr0.0830.21124
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218224
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021652
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_it1.9412.8453656
X-RAY DIFFRACTIONr_mcbond_other1.9412.8443655
X-RAY DIFFRACTIONr_mcangle_it3.2364.2574556
X-RAY DIFFRACTIONr_mcangle_other3.2364.2584557
X-RAY DIFFRACTIONr_scbond_it2.5283.1613625
X-RAY DIFFRACTIONr_scbond_other2.5273.1613626
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1534.6245337
X-RAY DIFFRACTIONr_long_range_B_refined6.22422.6527781
X-RAY DIFFRACTIONr_long_range_B_other6.20222.4077674
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A135990.04
12B135990.04
21A135140.06
22C135140.06
31A137150.03
32D137150.03
41B135780.05
42C135780.05
51B135740.04
52D135740.04
61C134640.06
62D134640.06
LS refinement shellResolution: 2.498→2.562 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 172 -
Rwork0.34 3232 -
obs--97.31 %
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)
12.4062-0.766-0.74012.11250.71192.28640.01820.28950.0361-0.1420.0297-0.1987-0.02530.181-0.04790.0591-0.0304-0.00530.11760.0480.08912.3403-42.6426-21.4288
21.8558-0.23920.21952.35270.73762.5350.07910.2252-0.0656-0.1697-0.1008-0.21010.10640.12960.02170.04450.00160.03140.13420.05010.085731.7717-56.8619-9.8519
32.15270.11320.03462.5794-0.69072.4918-0.0006-0.2475-0.07590.062-0.00150.09490.0765-0.12840.00210.01570.0127-0.00830.0776-0.03670.0633-16.0208-45.99566.4161
42.95760.2445-0.28412.2698-0.50132.3509-0.0895-0.16830.08950.14770.11880.148-0.0672-0.148-0.02920.05550.0344-0.03760.044-0.03190.081916.3439-46.166417.9141
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 239
2X-RAY DIFFRACTION2B1 - 239
3X-RAY DIFFRACTION3C1 - 239
4X-RAY DIFFRACTION4D1 - 239

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