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- PDB-6kbu: Crystal structure of yedK -

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Basic information

Entry
Database: PDB / ID: 6kbu
TitleCrystal structure of yedK
ComponentsSOS response-associated protein
KeywordsDNA BINDING PROTEIN / DNA repair. abasic site.
Function / homology
Function and homology information


: / protein-DNA covalent cross-linking activity / Lyases / protein-DNA covalent cross-linking repair / SOS response / Hydrolases; Acting on peptide bonds (peptidases) / peptidase activity / single-stranded DNA binding / DNA damage response / proteolysis
Similarity search - Function
SOS response associated peptidase-like / hypothetical protein yedk fold / SOS response associated peptidase (SRAP) / SOS response associated peptidase-like / SOS response associated peptidase (SRAP) / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Abasic site processing protein / Abasic site processing protein YedK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWang, N. / Bao, H. / Huang, H.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2018YFC1004500 China
National Natural Science Foundation of Chinathe Thousand Young Talents Program China
National Natural Science Foundation of China31800619 China
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Molecular basis of abasic site sensing in single-stranded DNA by the SRAP domain of E. coli yedK.
Authors: Wang, N. / Bao, H. / Chen, L. / Liu, Y. / Li, Y. / Wu, B. / Huang, H.
History
DepositionJun 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
B: SOS response-associated protein
A: SOS response-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5444
Polymers55,3602
Non-polymers1842
Water4,882271
1
B: SOS response-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7722
Polymers27,6801
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10100 Å2
MethodPISA
2
A: SOS response-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7722
Polymers27,6801
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-0 kcal/mol
Surface area10040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.740, 67.327, 74.875
Angle α, β, γ (deg.)90.000, 98.840, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SOS response-associated protein / yedk


Mass: 27680.111 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: yedK, C4J69_22885, ECTO6_01993, EFV06_12905, EFV16_12155, SAMEA3472108_01185, SAMEA3752559_04370
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A2S5ZH06, UniProt: P76318*PLUS, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 41.51 %
Crystal growTemperature: 293 K / Method: evaporation / Details: 0.2 M DL-malic acid pH7.0, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 26234 / % possible obs: 97.4 % / Redundancy: 5.2 % / Biso Wilson estimate: 25.03 Å2 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.072 / Rrim(I) all: 0.174 / Χ2: 0.986 / Net I/σ(I): 3.9 / Num. measured all: 136928
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.184.10.46223450.7680.2390.5240.97688.7
2.18-2.264.30.44725130.790.2260.5031.02593.7
2.26-2.374.50.38725750.8580.1930.4350.99796.6
2.37-2.495.20.35527080.9140.1660.3931.02199.9
2.49-2.655.40.31126740.9250.1450.3451.01899.7
2.65-2.855.50.2526400.9540.1150.2761.04499.2
2.85-3.145.30.18726840.9720.0860.2071.04698.7
3.14-3.595.90.14327010.9850.0630.1571.00899.8
3.59-4.525.70.10726380.9890.0470.1170.94398.1
4.52-4060.09527560.9950.0410.1030.81999.3

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX(1.12_2829: ???)refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ICU

2icu


Resolution: 2.1→38.085 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 23.91
RfactorNum. reflection% reflection
Rfree0.2401 1214 5.06 %
Rwork0.1667 --
obs0.1703 23970 88.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.7 Å2 / Biso mean: 29.624 Å2 / Biso min: 11.25 Å2
Refinement stepCycle: final / Resolution: 2.1→38.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3364 0 12 271 3647
Biso mean--47.28 32.58 -
Num. residues----427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073468
X-RAY DIFFRACTIONf_angle_d0.8534712
X-RAY DIFFRACTIONf_chiral_restr0.05488
X-RAY DIFFRACTIONf_plane_restr0.005628
X-RAY DIFFRACTIONf_dihedral_angle_d12.9932059
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0976-2.18150.2661040.18161714181862
2.1815-2.28080.284870.19122041212871
2.2808-2.40110.27871330.19282286241981
2.4011-2.55150.26941470.19072586273391
2.5515-2.74840.2951570.20172755291297
2.7484-3.02490.24951310.18352815294698
3.0249-3.46230.25121650.164128212986100
3.4623-4.36120.20891390.13882836297599
4.3612-38.09160.1971510.15182902305399
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)
12.1534-2.55930.43833.9498-1.19192.77010.1546-0.07760.0065-0.09520.1146-0.0547-0.39660.062-0.19310.1929-0.03360.02320.1927-0.04690.1998-7.7166-7.233381.7856
21.50290.5332-2.46212.2084-0.92594.03640.1621-0.2890.26010.4380.06920.2198-0.4314-0.0094-0.2350.22550.00040.01510.212-0.01520.2259-14.1328-8.440890.1467
30.77650.12980.14482.45070.70522.28250.01290.00320.0020.10360.0516-0.00290.266-0.0106-0.02780.1291-0.01540.01150.15140.0220.1628-8.3831-20.420275.1739
46.0416-0.20551.48763.5308-1.92124.0789-0.36440.1526-0.3706-0.05990.0949-0.33640.36110.33740.14470.1988-0.01180.03870.2677-0.01850.27035.8676-6.412470.1685
50.84091.094-0.70822.9691-1.36312.7292-0.08480.0637-0.1717-0.3281-0.0487-0.16710.16620.06930.17590.14320.0180.01280.1426-0.00480.1538-5.2498-14.878571.4209
62.95641.4682-0.27864.7242.57576.14010.0109-0.28180.2679-0.0277-0.16150.4139-0.0891-0.6180.1410.14560.0409-0.04630.22330.03780.2554-18.562-13.110768.939
72.5681-1.16111.98892.086-2.02724.2284-0.02250.08050.17410.1378-0.1343-0.2873-0.07330.39140.13770.1582-0.01220.02780.1959-0.02330.23895.7111-4.78374.5372
86.7604-0.682.49892.13440.4162.92690.20370.2426-0.2999-0.3478-0.00720.02680.48060.128-0.12710.3340.01210.0190.2421-0.00920.1725-11.7901-14.52943.285
93.21870.48031.14930.52830.04363.09030.0894-0.3379-0.08020.0417-0.0220.00070.0011-0.0611-0.06870.25590.0140.05130.1734-0.01460.2102-11.7346-9.279747.5219
100.74860.2788-0.25631.3926-0.07332.81760.1380.07940.0733-0.1091-0.0075-0.0332-0.2848-0.0029-0.13070.30780.01590.06240.1504-0.02230.2021-6.8-0.112235.3557
110.83740.4892-0.24651.48920.55922.5823-0.06650.12320.0678-0.14860.07680.0523-0.0899-0.2011-0.01160.2180.01660.01410.20380.03140.195-13.9693-9.189331.3029
126.00812.5711-0.35055.9112-0.5456.0565-0.0869-0.3298-0.13670.3739-0.0157-0.4060.00930.48720.07480.22030.0398-0.01360.2054-0.04660.21492.6703-8.856534.2123
135.1437-1.1383-1.58662.07390.40823.3405-0.0474-0.2750.04440.1102-0.01890.33570.0989-0.50460.08050.2671-0.0451-0.0190.3172-0.03190.2191-22.8287-16.702832.2781
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 2 through 20 )B2 - 20
2X-RAY DIFFRACTION2chain 'B' and (resid 21 through 33 )B21 - 33
3X-RAY DIFFRACTION3chain 'B' and (resid 34 through 101 )B34 - 101
4X-RAY DIFFRACTION4chain 'B' and (resid 102 through 120 )B102 - 120
5X-RAY DIFFRACTION5chain 'B' and (resid 121 through 164 )B121 - 164
6X-RAY DIFFRACTION6chain 'B' and (resid 165 through 191 )B165 - 191
7X-RAY DIFFRACTION7chain 'B' and (resid 192 through 222 )B192 - 222
8X-RAY DIFFRACTION8chain 'A' and (resid 2 through 20 )A2 - 20
9X-RAY DIFFRACTION9chain 'A' and (resid 21 through 50 )A21 - 50
10X-RAY DIFFRACTION10chain 'A' and (resid 51 through 102 )A51 - 102
11X-RAY DIFFRACTION11chain 'A' and (resid 103 through 164 )A103 - 164
12X-RAY DIFFRACTION12chain 'A' and (resid 165 through 192 )A165 - 192
13X-RAY DIFFRACTION13chain 'A' and (resid 193 through 222 )A193 - 222

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