PDB-6tyx: Structure of Ku80 von Willebrand domain S229A mutant complexed wi...

ID or keywords:

Entry

Database: PDB / ID: 6tyx

Title

Structure of Ku80 von Willebrand domain S229A mutant complexed with XLF Ku Binding Motif

Components

LYS-GLY-LEU-PHE-MET
X-ray repair cross-complementing protein 5

Keywords

DNA BINDING PROTEIN / Ku80 von Willebrand factor A domain / Fluorine-19 NMR / Ku binding motif / Conditional binding site

Function / homology

Function and homology information

Ku70:Ku80 complex / telomeric DNA binding / DNA helicase activity / telomere maintenance / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / double-strand break repair via nonhomologous end joining / double-strand break repair / DNA recombination / damaged DNA binding / hydrolase activity ...
Similarity search - Function

Biological species

Xenopus laevis (African clawed frog)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.89944353227 Å

Authors

Min, J. / Pedersen, L.C.

Funding support

United States, 1items

Citation

Journal: DNA Repair (Amst.) / Year: 2019
Title: Ligand binding characteristics of the Ku80 von Willebrand domain.
Authors: Kim, K. / Min, J. / Kirby, T.W. / Gabel, S.A. / Pedersen, L.C. / London, R.E.

History

Deposition	Aug 9, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 27, 2019	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6tyx.cif.gz	288 KB	Display	PDBx/mmCIF format
PDB format	pdb6tyx.ent.gz	212.4 KB	Display	PDB format
PDBx/mmJSON format	6tyx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6tyx_validation.pdf.gz	254.3 KB	Display	wwPDB validaton report
Full document	6tyx_full_validation.pdf.gz	254.2 KB	Display
Data in XML	6tyx_validation.xml.gz	937 B	Display
Data in CIF	6tyx_validation.cif.gz	6.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ty/6tyx ftp://data.pdbj.org/pub/pdb/validation_reports/ty/6tyx	HTTPS FTP

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Related structure data

Related structure data	6tytC 6tyuC 6tyvC 6tywC 6tyzSC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6mgy-3 6q30-1 6tgd-1 6ex7-1 1wy7-1 6q2y-2 6q30-2 6twt-2 4eyb-2 1gg6-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#55 - Jul 2004 DNA Ligase similarity (14) #134 - Feb 2011 Integrin similarity (1) #166 - Oct 2013 Proteasome similarity (1)

Deposited unit

A: X-ray repair cross-complementing protein 5

B: X-ray repair cross-complementing protein 5

C: LYS-GLY-LEU-PHE-MET

D: LYS-GLY-LEU-PHE-MET

56.2 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: X-ray repair cross-complementing protein 5

C: LYS-GLY-LEU-PHE-MET

defined by author&software
Evidence: gel filtration
28.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: X-ray repair cross-complementing protein 5

D: LYS-GLY-LEU-PHE-MET

defined by author&software
28.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	44.798, 71.605, 74.600
Angle α, β, γ (deg.)	90.000, 98.309, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	X-ray repair cross-complementing protein 5 Mass: 26169.980 Da / Num. of mol.: 2 / Fragment: Ku80 von Willebrand / Mutation: C190S, S229A, deletion loop (E171 through R188) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: XELAEV_18044412mg / Production host: Escherichia coli (E. coli) References: UniProt: A0A1L8EVE5, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein/peptide	LYS-GLY-LEU-PHE-MET Mass: 1918.394 Da / Num. of mol.: 2 / Fragment: APLF Ku Binding Motif / Source method: obtained synthetically / Source: (synth.) Xenopus laevis (African clawed frog) / References: UniProt: A0A1L8ENT6*PLUS
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 1.98 Å³/Da / Density % sol: 37.85 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES NaOH pH 7.5, 25 % (w/v) PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
Detector	Type: RIGAKU SATURN 944 / Detector: CCD / Date: May 20, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 1.89→50 Å / Num. obs: 36348 / % possible obs: 98.6 % / Redundancy: 4.1 % / B_iso Wilson estimate: 29.7417965936 Å² / R_rim(I) all: 0.05 / Net I/σ(I): 39.7
Reflection shell	Resolution: 1.9→1.93 Å / Num. unique obs: 1765 / R_rim(I) all: 0.335

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Processing

Software

Name	Version	Classification
PHENIX	1.10.1_2155	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6TYZ

6tyz

Resolution: 1.89944353227→40.685646148 Å / SU ML: 0.214299439303 / Cross valid method: FREE R-VALUE / σ(F): 1.33619816583 / Phase error: 24.2090853008
Details: The model of the 6xHis-tag in Chain B is based on the best guess for the discontinuous electron density.

	R_factor	Num. reflection	% reflection
R_free	0.225010419974	1813	4.99862145023 %
R_work	0.184601605569	-	-
obs	0.186661278414	36270	98.2181542461 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 48.8112569487 Å²

Refinement step

Cycle: LAST / Resolution: 1.89944353227→40.685646148 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3297	0	0	228	3525

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0042989708223	3432
X-RAY DIFFRACTION	f_angle_d	0.647134876889	4654
X-RAY DIFFRACTION	f_chiral_restr	0.0433272526973	552
X-RAY DIFFRACTION	f_plane_restr	0.00375229952194	603
X-RAY DIFFRACTION	f_dihedral_angle_d	13.3251140769	1200

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.8995-1.9508	0.27654991736	132	0.267097081684	2504	X-RAY DIFFRACTION	92.2646132307
1.9508-2.0082	0.278381811453	134	0.245501729116	2545	X-RAY DIFFRACTION	95.6444127097
2.0082-2.073	0.284073074687	137	0.208292089629	2603	X-RAY DIFFRACTION	97.439544808
2.073-2.1471	0.220072313243	139	0.205554185139	2640	X-RAY DIFFRACTION	98.1285310734
2.1471-2.2331	0.264965632358	140	0.195298942798	2652	X-RAY DIFFRACTION	98.3098591549
2.2331-2.3347	0.22691971609	139	0.207098121045	2639	X-RAY DIFFRACTION	98.197242842
2.3347-2.4578	0.241197537714	141	0.192922245967	2666	X-RAY DIFFRACTION	99.2574257426
2.4578-2.6117	0.224945220066	140	0.197582462295	2672	X-RAY DIFFRACTION	99.7163120567
2.6117-2.8133	0.256524517347	142	0.206106765292	2704	X-RAY DIFFRACTION	99.3715083799
2.8133-3.0964	0.245522281446	139	0.211394071276	2657	X-RAY DIFFRACTION	99.1841078397
3.0964-3.5442	0.221634472198	142	0.179407719757	2710	X-RAY DIFFRACTION	99.9649491763
3.5442-4.4644	0.190811568728	142	0.151390189822	2716	X-RAY DIFFRACTION	99.8253580161
4.4644-40.6856	0.20936487437	146	0.16664573374	2749	X-RAY DIFFRACTION	99.5872033024

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	7.06743792966	-3.16356716441	-0.159061165344	5.03335578841	0.171689351022	3.64373233001	-0.0632671225783	0.223548856029	0.229504709633	0.438495846597	-0.208027429361	-0.31513695626	-0.419426903993	-0.555564623539	-0.024817688819	0.240943399183	0.0246752830285	-0.00496860563789	0.132647127332	0.0090418200385	0.21415218904	12.5452429902	6.10794404986	-0.865200964879
2	3.24623728593	-0.280934156246	-0.267374118477	0.184995500933	-0.0698393333692	0.0726773874529	0.122972098227	0.173802949173	-0.386213318141	-0.0931679749946	-0.0980350125559	-0.117296763631	0.665259233239	0.204631852931	0.0734250455603	0.426424821875	0.0338775617736	0.00217912159238	0.125447131177	-0.00613432045646	0.342954410942	20.4187626271	-13.1774541422	-7.90025199645
3	7.14467221299	-5.50048566259	2.34508723224	6.38752235008	-2.29023275348	4.41755357743	0.10402010279	0.00908740271786	-0.125515452428	-0.270382424963	0.0340533542763	0.106853342854	0.187309316012	-0.423947375382	-0.0292762188222	0.203361287806	-0.0123591790481	-0.0100359720357	0.216565049692	-0.0207071775207	0.247273720831	8.79092337021	-0.677318150303	-9.27805936194
4	1.1835731652	1.44957475372	-0.415739451549	2.24672670447	0.609732680474	3.09213795929	-0.0581823088046	0.0498392592794	0.421792375447	-0.234803545377	-0.0763386879461	-0.347177878297	-0.436372056116	-0.0826005084066	0.108280747275	0.294912870526	0.0181101520757	-0.0146233830257	0.130999527427	-0.0115243919397	0.328693544957	18.3762965448	8.11649866157	-4.01224118816
5	1.36957483662	-0.0280320297574	-0.145633459516	2.75352328373	0.367847421544	2.28641592654	-0.0792125497508	-0.0225053580301	0.102543318998	0.0799120780441	0.0170847909719	-0.361889537325	-0.301249027472	0.0954400006722	0.067047019864	0.202248654384	-0.00388594647072	-0.00352131717571	0.0976761903427	0.0103213532972	0.32612958882	20.3808137982	6.5326100292	-3.93936015833
6	0.244233226837	0.0148919706181	0.0630895839329	3.81374321865	0.461548640617	2.17141703789	-0.148206485487	-0.213938053666	0.624616095515	0.0939486513418	0.183146954558	-0.453873016366	0.0263470863501	-0.0139834643474	0.0585618879488	0.187185039236	0.0191267336323	-0.0136480630201	0.142864258678	-0.0422585636348	0.391598605744	16.4995354559	2.58958627805	4.83149010085
7	2.475860346	-0.477999925772	0.796390311866	5.33999587179	1.47542214355	4.02612544064	-0.202433348925	-0.409047192839	-0.0634457439085	0.418424133457	0.228129227318	-0.0589707987736	0.00189138204968	0.0300607561435	0.00426583621708	0.183854062428	0.0265995265403	0.0350694005038	0.198296012439	0.0131560150169	0.184142131651	14.6991461474	-2.8427051636	9.80255898852
8	2.49349233768	-0.77721411458	1.14855734959	3.48494641794	-0.19467435695	6.25895510674	-0.036240383318	-0.187517973925	-0.0995677304614	0.217083937741	0.258686720619	0.303006717391	0.0153076840193	-0.530527347291	-0.176500902895	0.239292197038	-0.0523971927112	0.0808384456325	0.21472562902	0.0309267113081	0.308461666556	9.86006744545	-6.37741099979	6.63220544832
9	0.958302078267	0.287414171904	0.577798453761	4.64045134247	5.73413525609	7.28831609712	0.477224435216	-0.513440682929	-0.92730158895	-0.182481659746	-1.12814316044	1.04165367816	0.561224947152	-1.45578555226	0.619588287756	0.828620991871	0.0720175517006	-0.207235571845	0.833394436646	-0.130446232726	0.954141264634	30.706254045	-21.5372850679	31.8992527419
10	2.15806675765	0.278935384205	0.13272910343	2.72737178557	0.217667577615	3.4391826904	0.0986008861905	0.468882982184	0.0239932850756	-0.0227714748457	-0.113584244851	-0.221235557663	-0.236181843921	0.264255568191	0.0828378792236	0.223853430136	0.0180103885035	-0.00548132575466	0.416051895071	0.00688712041025	0.231295220925	32.4441414855	13.8277211779	42.5965361731
11	1.76185128344	-0.277745398609	-0.134688807903	6.51737113511	-1.90301254299	5.49920261321	0.101765226802	0.692308799135	0.12673697701	0.301637077952	-0.324280436553	-0.802343538927	-0.277035797851	0.751280685109	-0.0953249394778	0.176754318285	0.0189030142457	-0.0231491340844	0.474116003728	-0.0131968581634	0.34365987114	40.9879545391	7.48294925431	47.4397231139
12	1.42621296062	-0.161722658045	0.211126978925	2.10540347674	-0.313251023035	2.73359852382	0.219824520064	0.94411385533	-0.208917370055	-0.494609572583	-0.306237584025	0.112203936112	0.00494498673856	-0.0979402240089	-0.059550187773	0.340854187444	0.0904854441326	-0.0668965741442	0.567654598918	-0.0688269584699	0.274816247458	25.4789004839	10.3109066277	35.062108775
13	4.61671236281	0.383404193796	0.546567830623	4.69564109298	-0.232489792149	4.20603488663	0.124571172118	0.371232578371	-0.38553003918	-0.177402970144	-0.150832202306	0.698757528661	0.00904904713649	-0.320832381599	-0.10797861292	0.211971268949	0.0406406771544	-0.0202640355506	0.522232440763	-0.0846648633203	0.388782351521	16.5376248817	10.416069605	42.8235074472
14	9.55335381252	-0.47261988816	-5.83540085916	0.0665726712496	0.778880705196	8.99108723203	0.446816161608	-0.52343567606	1.83687795142	0.521494814682	-0.038280161114	1.45496379466	-0.609344865978	-1.43403495847	-0.235755327148	0.278081636585	-0.00581921372215	0.0673236152504	0.554788971523	-0.0439016608487	0.793998571964	2.00056323669	2.10479445267	1.03236051652
15	1.93169383327	-1.94657650589	-1.78688475576	4.00252735646	4.32009120574	4.85692272035	-0.70781011668	-0.857747703221	-0.670894072718	0.636950833537	0.736217800909	0.616016413366	1.7121309402	-0.117027396452	-0.341106755273	0.538466490406	0.0484308259684	-0.0476795945884	0.537523708856	0.0526985379569	0.620751292254	22.2087693531	0.200688027025	47.8044379981

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 14 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 15 through 28 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 29 through 46 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 47 through 68 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 69 through 120 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 121 through 142 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 143 through 197 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 198 through 237 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid -6 through 7 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 8 through 80 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 81 through 95 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 96 through 197 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 198 through 236 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 307 through 311 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 305 through 311 )

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