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- PDB-5nyw: Anbu (ancestral beta-subunit) from Yersinia bercovieri -

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Basic information

Entry
Database: PDB / ID: 5nyw
TitleAnbu (ancestral beta-subunit) from Yersinia bercovieri
ComponentsPeptidase
KeywordsUNKNOWN FUNCTION / ANBU / ANCESTRAL / PROTEASOME / BETA-SUBUNIT / 20S / HSLV / NTN-HYDROLASE
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 / AZIDE ION / DI(HYDROXYETHYL)ETHER / Peptidase
Function and homology information
Biological speciesYersinia bercovieri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å
AuthorsPiasecka, A. / Czapinska, H. / Vielberg, M. / Szczepanowski, R.H. / Reed, S. / Groll, M. / Bochtler, M.
Funding support Poland, United Kingdom, 2items
OrganizationGrant numberCountry
National Science CentreNCN UMO-2013/08/S/NZ1/00681 Poland
Cardiff University United Kingdom
CitationJournal: J. Mol. Biol. / Year: 2018
Title: The Y. bercovieri Anbu crystal structure sheds light on the evolution of highly (pseudo)symmetric multimers.
Authors: Piasecka, A. / Czapinska, H. / Vielberg, M.T. / Szczepanowski, R.H. / Kiefersauer, R. / Reed, S. / Groll, M. / Bochtler, M.
History
DepositionMay 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jan 3, 2018Group: Database references / Category: citation / citation_author
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
Revision 1.3Mar 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name
Revision 1.4Jan 31, 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
Revision 2.0Feb 5, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_type ...atom_site / atom_type / chem_comp / entity / entity_name_com / entity_src_gen / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_validate_close_contact / software / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.auth_atom_id / _atom_site.auth_comp_id ..._atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _software.classification / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidase
B: Peptidase
C: Peptidase
D: Peptidase
E: Peptidase
F: Peptidase
G: Peptidase
H: Peptidase
I: Peptidase
J: Peptidase
K: Peptidase
L: Peptidase
M: Peptidase
N: Peptidase
O: Peptidase
P: Peptidase
Q: Peptidase
R: Peptidase
S: Peptidase
T: Peptidase
U: Peptidase
V: Peptidase
W: Peptidase
X: Peptidase
Y: Peptidase
Z: Peptidase
1: Peptidase
2: Peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)790,12775
Polymers786,85228
Non-polymers3,27547
Water32,2471790
1
A: Peptidase
B: Peptidase
C: Peptidase
D: Peptidase
E: Peptidase
F: Peptidase
G: Peptidase
H: Peptidase
I: Peptidase
J: Peptidase
K: Peptidase
L: Peptidase
M: Peptidase
N: Peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)394,84736
Polymers393,42614
Non-polymers1,42222
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53580 Å2
ΔGint-356 kcal/mol
Surface area116990 Å2
MethodPISA
2
O: Peptidase
P: Peptidase
Q: Peptidase
R: Peptidase
S: Peptidase
T: Peptidase
U: Peptidase
V: Peptidase
W: Peptidase
X: Peptidase
Y: Peptidase
Z: Peptidase
1: Peptidase
2: Peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)395,27939
Polymers393,42614
Non-polymers1,85325
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53480 Å2
ΔGint-444 kcal/mol
Surface area117490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.535, 285.371, 179.213
Angle α, β, γ (deg.)90.00, 91.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 28 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZ12

#1: Protein ...
Peptidase


Mass: 28101.844 Da / Num. of mol.: 28
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia bercovieri (bacteria) / Gene: CS533_03425 / Plasmid: PET20B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2G4U6U6

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Non-polymers , 7 types, 1837 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 103.120 Da / Num. of mol.: 4 / Source method: isolated from a natural source
#6: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1790 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 3.36 Å3/Da / Density % sol: 63.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 0.1M BIS-TRIS PROPANE/HCL (pH 6.9); 18% w/v PEG 3350; 7.5% v/v ETHYLENE GLYCOL; 0.2M NA2SO4
PH range: 6.7 - 6.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97935 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 325849 / % possible obs: 98.9 % / Redundancy: 5.78 % / Rmerge(I) obs: 0.092 / Rsym value: 0.087 / Net I/σ(I): 14.63
Reflection shellResolution: 2.5→2.57 Å / Redundancy: 5.69 % / Rmerge(I) obs: 1.078 / Mean I/σ(I) obs: 2.06 / Rsym value: 0.98 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NYG

5nyg


Resolution: 2.501→49.185 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.42
Details: NCS restraints have been used. TLS refinement has been performed. The assignment of ions and PEG molecules is tentative only and their coordination is perturbed due to the limited resolution ...Details: NCS restraints have been used. TLS refinement has been performed. The assignment of ions and PEG molecules is tentative only and their coordination is perturbed due to the limited resolution (we have not restrained the protein-ion distances beyond the standard routines of the PHENIX software).
RfactorNum. reflection% reflectionSelection details
Rfree0.2298 1983 0.61 %THIN RESOLUTION SHELLS
Rwork0.1828 ---
obs0.1831 325791 99.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.501→49.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms50963 0 147 1790 52900
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00952028
X-RAY DIFFRACTIONf_angle_d1.25370397
X-RAY DIFFRACTIONf_dihedral_angle_d12.73519317
X-RAY DIFFRACTIONf_chiral_restr0.0547988
X-RAY DIFFRACTIONf_plane_restr0.0079128
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.501-2.56360.2814960.279222574X-RAY DIFFRACTION97
2.5636-2.63290.34421980.265723014X-RAY DIFFRACTION99
2.6329-2.71040.3525990.25123090X-RAY DIFFRACTION99
2.7104-2.79780.29752000.238323036X-RAY DIFFRACTION99
2.7978-2.89780.29461000.226723207X-RAY DIFFRACTION99
2.8978-3.01380.29861990.218422974X-RAY DIFFRACTION99
3.0138-3.1510.25731000.207423169X-RAY DIFFRACTION99
3.151-3.31710.2752990.208523268X-RAY DIFFRACTION99
3.3171-3.52480.2381980.185123114X-RAY DIFFRACTION99
3.5248-3.79690.20441000.171223242X-RAY DIFFRACTION99
3.7969-4.17880.21041990.160823153X-RAY DIFFRACTION99
4.1788-4.7830.2038990.151323281X-RAY DIFFRACTION99
4.783-6.02440.22841960.163723257X-RAY DIFFRACTION100
6.0244-49.1940.15291000.167223429X-RAY DIFFRACTION99
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)
11.2356-1.33360.38252.3459-0.01651.1913-0.0533-0.343-0.15410.12450.06450.26470.1676-0.3212-0.00470.4385-0.11110.14210.57340.05140.444915.3778-56.7981121.5795
21.47820.03770.97550.5387-0.02961.8276-0.0795-0.06880.2430.0591-0.03660.0323-0.0669-0.06840.10370.3065-0.02420.09030.5205-0.06330.63394.5079-33.147399.3657
31.1140.38730.56331.08950.37281.88230.00460.10140.0666-0.0445-0.0395-0.0574-0.11670.07160.04990.3166-0.03080.05120.40630.08120.570233.073-29.721281.6493
40.6716-0.24760.41.4085-0.68591.7845-0.0031-0.02240.01050.03470.03580.11230.00280.0707-0.03840.24330.00010.0350.4445-0.00060.531968.9738-49.898790.5683
51.69090.65120.42961.83170.44771.14890.02910.14280.0055-0.3227-0.0060.02630.05310.1041-0.03170.37450.0299-0.00120.43330.05570.33451.7292-48.637560.7201
62.07980.5866-0.03221.5620.25460.7825-0.11380.3641-0.0816-0.46540.0953-0.05370.2191-0.01030.00260.75610.0292-0.01730.5447-0.0150.368953.8196-81.28451.8939
71.3890.69670.12091.69510.26221.4383-0.06340.1606-0.2015-0.1889-0.0147-0.54730.10290.15210.0650.59190.16660.0980.4808-0.0050.64473.55-110.556875.5719
82.0703-0.1428-0.33671.5-0.24120.5997-0.14960.1482-0.0596-0.23280.1195-0.01680.1361-0.05270.03870.78690.0397-0.04770.5165-0.08950.346641.2097-110.096263.6254
91.4106-0.0205-0.1682.1655-0.2091.58020.01310.112-0.08640.15070.07070.1359-0.1562-0.1978-0.07690.53530.1173-0.05050.4283-0.07050.373625.4419-119.710291.6247
101.96050.3597-0.57141.4869-0.18240.64850.0564-0.1132-0.19280.3995-0.0609-0.0906-0.03830.04670.00550.77820.0372-0.10790.36410.05090.427244.2513-129.7702127.9284
111.3915-0.92360.29272.7346-0.140.8058-0.0501-0.1151-0.07630.28750.04730.1123-0.1072-0.02580.01990.7060.07680.09190.41760.0260.424919.7078-106.7072122.0086
121.7637-0.5020.25771.95920.62332.27680.0758-0.1232-0.16120.2480.0728-0.10240.43360.1045-0.12280.57640.0801-0.08760.3676-0.01950.449417.874635.0118215.871
131.4661-0.44430.48242.42670.06221.02060.08580.22060.023-0.0464-0.0697-0.33920.05850.255-0.00630.51250.09210.04880.52450.05510.447813.207349.9397186.2137
142.19490.26690.17771.30810.27491.2555-0.02160.13530.1805-0.0483-0.04150.0902-0.1026-0.05880.04480.52490.09730.01380.31890.04210.3429-18.500361.1739190.5787
152.2877-0.6178-0.16852.15280.59640.83270.04610.31780.1447-0.40960.0205-0.1259-0.08530.1409-0.05760.70180.07650.09180.61150.09050.3661-1.184242.538156.7589
161.75370.5862-0.49141.7997-0.04591.48470.10380.26930.0835-0.3304-0.17880.4053-0.2033-0.17670.07180.56480.2047-0.08450.5111-0.04730.4726-33.926442167.3226
171.51520.09880.1991.68970.06930.68130.04810.21260.067-0.4433-0.06990.0316-0.2363-0.00150.03320.75260.1545-0.00070.64170.01190.3541-13.544714.8137142.0109
180.1710.2520.09251.3064-0.09152.01380.03640.0897-0.0755-0.1007-0.08840.3573-0.0533-0.19750.07460.39190.1488-0.05950.5537-0.08490.5934-40.29449.0429163.2925
191.17540.6375-0.55651.8039-0.4741.4520.08490.21530.0247-0.2376-0.12250.1339-0.0583-0.19560.03360.38380.1221-0.02440.5559-0.09320.3743-11.8817-18.4596147.5829
200.5188-0.0702-0.48041.30810.7342.1420.03180.0402-0.0810.015-0.0512-0.0321-0.0606-0.11310.02590.29560.0348-0.03880.5366-0.0710.5968-29.425-19.6169177.2815
210.96640.4735-0.46711.3946-0.46832.210.02720.1056-0.086-0.0782-0.01-0.01570.09470.0212-0.01690.25550.0338-0.05550.3624-0.11230.43596.4411-39.3297166.8019
220.7636-0.19090.23052.31020.29071.7191-0.1249-0.15190.12140.20180.0404-0.0484-0.0702-0.0490.06580.3447-0.0294-0.06860.476-0.08510.4941-4.3853-28.6191197.6766
230.49110.0611-0.16262.456-0.73681.4955-0.0708-0.1488-0.02410.1887-0.02690.02080.02080.06760.07470.3153-0.03770.06440.43380.02130.464443.7149-42.6885111.4662
240.71010.26620.17541.01850.01142.01310.01340.11560.0885-0.10590.0042-0.39070.03120.2374-0.0020.4430.11810.06350.51670.00640.681679.9992-77.442674.2015
251.62360.8313-0.09141.1795-0.01031.0311-0.01560.055-0.29410.0507-0.0585-0.31150.01990.12060.07620.60590.099-0.05380.3625-0.0270.580457.0806-131.415496.5805
261.67480.02920.10030.95660.0290.71970.02910.08680.05790.07650.0834-0.07410.0761-0.0173-0.10430.60390.03580.03690.360.0080.3614-7.965356.926222.151
270.9080.21-0.68451.0247-0.19372.6175-0.12050.0558-0.1280.07180.0079-0.18250.05710.0250.12570.28090.0173-0.07840.4910.00920.556234.9778-37.1915184.7086
282.0366-1.21250.1172.26580.30271.0947-0.141-0.48160.41880.24330.1081-0.3515-0.23140.17850.04860.4897-0.0579-0.14230.6076-0.09920.5423.627-15.7572209.5116
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 242)
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 242)
3X-RAY DIFFRACTION3(chain 'D' and resid 1 through 242)
4X-RAY DIFFRACTION4(chain 'E' and resid 1 through 241)
5X-RAY DIFFRACTION5(chain 'F' and resid 1 through 242)
6X-RAY DIFFRACTION6(chain 'H' and resid 1 through 241)
7X-RAY DIFFRACTION7(chain 'I' and resid 1 through 241)
8X-RAY DIFFRACTION8(chain 'J' and resid 1 through 242)
9X-RAY DIFFRACTION9(chain 'L' and resid 1 through 243)
10X-RAY DIFFRACTION10(chain 'M' and resid 1 through 242)
11X-RAY DIFFRACTION11(chain 'N' and resid 1 through 241)
12X-RAY DIFFRACTION12(chain 'O' and resid 1 through 242)
13X-RAY DIFFRACTION13(chain 'Q' and resid 1 through 243)
14X-RAY DIFFRACTION14(chain 'R' and resid 1 through 243)
15X-RAY DIFFRACTION15(chain 'S' and resid 1 through 242)
16X-RAY DIFFRACTION16(chain 'T' and resid 1 through 242)
17X-RAY DIFFRACTION17(chain 'U' and resid 1 through 242)
18X-RAY DIFFRACTION18(chain 'V' and resid 1 through 241)
19X-RAY DIFFRACTION19(chain 'W' and resid 1 through 241)
20X-RAY DIFFRACTION20(chain 'X' and resid 1 through 242)
21X-RAY DIFFRACTION21(chain 'Y' and resid 1 through 241)
22X-RAY DIFFRACTION22(chain 'Z' and resid 1 through 242)
23X-RAY DIFFRACTION23(chain 'C' and resid 1 through 243)
24X-RAY DIFFRACTION24(chain 'G' and resid 1 through 242)
25X-RAY DIFFRACTION25(chain 'K' and resid 1 through 241)
26X-RAY DIFFRACTION26(chain 'P' and resid 1 through 241)
27X-RAY DIFFRACTION27(chain '1' and resid 1 through 242)
28X-RAY DIFFRACTION28(chain '2' and resid 1 through 241)

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