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- PDB-6sj9: Proteasome accessory factor B/C (PafBC) of Arthrobacter aurescens -

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Basic information

Entry
Database: PDB / ID: 6sj9
TitleProteasome accessory factor B/C (PafBC) of Arthrobacter aurescens
ComponentsProteasome accessory factor B/C (PafBC)
KeywordsTRANSCRIPTION / transcriptional regulator / DNA damage response / Sm-fold / winged helix-turn-helix / WYL domain / ferredoxin-like fold
Function / homologyPafC, HTH domain / PafC helix-turn-helix domain / : / WYL domain / WYL domain / : / DI(HYDROXYETHYL)ETHER / THIOCYANATE ION / WYL domain-containing protein
Function and homology information
Biological speciesPaenarthrobacter aurescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsMueller, A.U. / Leibundgut, M. / Ban, N. / Weber-Ban, E.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A-163314 Switzerland
CitationJournal: Nat Commun / Year: 2019
Title: Structure and functional implications of WYL domain-containing bacterial DNA damage response regulator PafBC.
Authors: Muller, A.U. / Leibundgut, M. / Ban, N. / Weber-Ban, E.
History
DepositionAug 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _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: Proteasome accessory factor B/C (PafBC)
B: Proteasome accessory factor B/C (PafBC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,35211
Polymers146,5392
Non-polymers8139
Water4,756264
1
A: Proteasome accessory factor B/C (PafBC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8797
Polymers73,2691
Non-polymers6106
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Proteasome accessory factor B/C (PafBC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4734
Polymers73,2691
Non-polymers2033
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.875, 119.033, 160.212
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 64 or resid 76...
21(chain B and (resid 2 through 121 or resid 132...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAMSEMSE(chain A and (resid 2 through 64 or resid 76...AA2 - 642 - 64
12SERSERPHEPHE(chain A and (resid 2 through 64 or resid 76...AA76 - 22476 - 224
13PROPROMSEMSE(chain A and (resid 2 through 64 or resid 76...AA226 - 45226 - 45
14SERSERGLUGLU(chain A and (resid 2 through 64 or resid 76...AA454 - 487454 - 487
15ALAALASERSER(chain A and (resid 2 through 64 or resid 76...AA489 - 664489 - 664
21ALAALAVALVAL(chain B and (resid 2 through 121 or resid 132...BB2 - 1212 - 121
22ASPASPPHEPHE(chain B and (resid 2 through 121 or resid 132...BB132 - 224132 - 224
23PROPROGLUGLU(chain B and (resid 2 through 121 or resid 132...BB226 - 487226 - 487
24ALAALASERSER(chain B and (resid 2 through 121 or resid 132...BB489 - 664489 - 664

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Proteasome accessory factor B/C (PafBC)


Mass: 73269.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenarthrobacter aurescens (bacteria) / Gene: AAur_2182 / Variant: 579 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: A0A4Y3NDN0*PLUS

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Non-polymers , 5 types, 273 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.55 Å3/Da / Density % sol: 51.67 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 100 mM Bis-Tris-propane pH 8.8 to 9.2, 80-160 mM KSCN, 18-21% w/v PEG-2000
PH range: 8.8 - 9.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.978561 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978561 Å / Relative weight: 1
ReflectionResolution: 2.1→48.725 Å / Num. obs: 87298 / % possible obs: 99.9 % / Redundancy: 67.7 % / CC1/2: 1 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.017 / Rrim(I) all: 0.145 / Net I/σ(I): 27.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.1-2.1458.95.3442990.4980.6845.38597.5
11.32-48.72561.10.05665510.0070.05798.9

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
XDSVERSION Jan 26, 2018 BUILT=20180808data reduction
SHELXCD2016/1phasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→48.725 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 26.83
RfactorNum. reflection% reflection
Rfree0.2375 7292 4.99 %
Rwork0.2032 --
obs0.2049 76278 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 211.32 Å2 / Biso mean: 74.6171 Å2 / Biso min: 26.67 Å2
Refinement stepCycle: final / Resolution: 2.2→48.725 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9923 0 49 264 10236
Biso mean--88.63 52.48 -
Num. residues----1279
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5767X-RAY DIFFRACTION13.32TORSIONAL
12B5767X-RAY DIFFRACTION13.32TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.2-2.2250.35552470.29734685
2.225-2.25120.35872380.29554578
2.2512-2.27860.2942440.27374674
2.2786-2.30750.32382370.26854565
2.3075-2.33780.33892420.27314660
2.3378-2.36990.29672420.26154622
2.3699-2.40370.31482450.25284644
2.4037-2.43960.27362410.24344591
2.4396-2.47770.25892430.24084633
2.4777-2.51830.27292460.244630
2.5183-2.56180.26762400.23284573
2.5618-2.60830.27522490.24244664
2.6083-2.65850.28732420.24044645
2.6585-2.71280.31362450.24354589
2.7128-2.77180.29272440.24794620
2.7718-2.83620.29172430.24074630
2.8362-2.90710.31972380.24594636
2.9071-2.98570.30032450.24894630
2.9857-3.07360.29162400.24884589
3.0736-3.17280.33852400.24074644
3.1728-3.28610.2612450.23284621
3.2861-3.41770.30072480.22244661
3.4177-3.57320.25332430.22674633
3.5732-3.76150.22772450.20454600
3.7615-3.99710.21132450.18094589
3.9971-4.30550.16282430.16154657
4.3055-4.73850.16782410.14684608
4.7385-5.42340.19612420.16314634
5.4234-6.82990.21312430.18724610
6.8299-48.7250.17942460.15854614
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)
12.5379-1.2006-1.35040.89421.31272.16930.2882-0.0940.2503-0.256-0.1382-0.1582-0.4151-0.1982-0.17430.4510.04760.06510.37380.11150.475320.390660.559473.1981
22.1252-0.6679-0.64661.66260.52661.25160.30590.29520.1984-0.3846-0.14790.1213-0.0658-0.1583-0.14050.42460.0666-0.0160.36870.05350.416919.965548.92461.5967
30.7504-0.1416-0.49840.894-0.97731.32520.11750.188-0.134-0.11050.07430.38090.1629-0.1983-0.18930.3212-0.0081-0.06210.336-0.00690.42128.425240.786379.5643
45.44470.08260.65467.31843.59058.03930.12881.1703-1.6969-0.45860.2794-0.93230.10210.4913-0.34990.5212-0.03620.02231.0732-0.3311.0272-20.468461.944274.2252
54.1116-1.1547-0.70573.5036-0.03563.42330.0812-0.130.3530.07060.210.252-0.6973-0.0462-0.24870.4971-0.0102-0.02060.42280.05340.4965-26.056790.2337106.9689
61.55360.3769-0.01222.07320.75581.6998-0.02080.35560.1512-0.55960.01950.4191-0.4467-0.2553-0.07040.57290.0779-0.08960.43090.08660.4347-21.321189.1312106.0809
74.5771-0.8863-4.11124.04012.33087.19330.11220.5596-0.0659-0.6220.19640.1608-0.3611-0.2008-0.30360.3989-0.0348-0.13640.6081-0.0440.5646-25.819476.632994.5986
83.46170.7795-1.23743.47970.31361.9633-1.069-0.6156-0.29831.55991.65420.20410.0238-0.48440.43661.26590.78440.33960.83720.25250.7925-6.36256.1191109.2491
92.1574-2.9317-0.08584.1587-0.6982.2185-0.02130.0197-0.78170.4218-0.01450.52681.0770.02920.03250.59120.00330.05560.4358-0.04130.7143-16.023764.8166116.774
106.07581.67720.15966.0866-0.70464.10910.02910.33230.0603-0.2880.01810.0704-0.19670.0036-0.06140.24280.06670.00220.2444-0.00710.24-11.484986.1452118.2083
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 211 )A1 - 211
2X-RAY DIFFRACTION2chain 'A' and (resid 212 through 426 )A212 - 426
3X-RAY DIFFRACTION3chain 'A' and (resid 427 through 664 )A427 - 664
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 94 )B2 - 94
5X-RAY DIFFRACTION5chain 'B' and (resid 95 through 211 )B95 - 211
6X-RAY DIFFRACTION6chain 'B' and (resid 212 through 377 )B212 - 377
7X-RAY DIFFRACTION7chain 'B' and (resid 378 through 476 )B378 - 476
8X-RAY DIFFRACTION8chain 'B' and (resid 477 through 559 )B477 - 559
9X-RAY DIFFRACTION9chain 'B' and (resid 560 through 593 )B560 - 593
10X-RAY DIFFRACTION10chain 'B' and (resid 594 through 664 )B594 - 664

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