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- PDB-3kgv: Crystal Structure of Human DNA-dependent Protein Kinase Catalytic... -

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Basic information

Entry
Database: PDB / ID: 3kgv
TitleCrystal Structure of Human DNA-dependent Protein Kinase Catalytic Subunit (DNA-PKcs)
ComponentsDNA-dependent Protein Kinase Catalytic Subunit
KeywordsTRANSFERASE / DNA-dependent Protein Kinase Catalytic Subunit / DNA-PKcs / Ku80 / non-homologues end joining / DNA repair
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 6.6 Å
AuthorsSibanda, B.L. / Chirgadze, D.Y. / Blundell, T.L.
CitationJournal: Nature / Year: 2010
Title: Crystal structure of DNA-PKcs reveals a large open-ring cradle comprised of HEAT repeats.
Authors: Sibanda, B.L. / Chirgadze, D.Y. / Blundell, T.L.
History
DepositionOct 29, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 23, 2014Group: Other
Revision 1.3Nov 20, 2019Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.content_type
Revision 1.4Mar 20, 2024Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-dependent Protein Kinase Catalytic Subunit
B: DNA-dependent Protein Kinase Catalytic Subunit
C: DNA-dependent Protein Kinase Catalytic Subunit
D: DNA-dependent Protein Kinase Catalytic Subunit
E: DNA-dependent Protein Kinase Catalytic Subunit
F: DNA-dependent Protein Kinase Catalytic Subunit
X: DNA-dependent Protein Kinase Catalytic Subunit
O: DNA-dependent Protein Kinase Catalytic Subunit
P: DNA-dependent Protein Kinase Catalytic Subunit
Q: DNA-dependent Protein Kinase Catalytic Subunit
R: DNA-dependent Protein Kinase Catalytic Subunit
S: DNA-dependent Protein Kinase Catalytic Subunit
T: DNA-dependent Protein Kinase Catalytic Subunit
Y: DNA-dependent Protein Kinase Catalytic Subunit


Theoretical massNumber of molelcules
Total (without water)4,918,80714
Polymers4,918,80714
Non-polymers00
Water0
1
A: DNA-dependent Protein Kinase Catalytic Subunit
B: DNA-dependent Protein Kinase Catalytic Subunit
C: DNA-dependent Protein Kinase Catalytic Subunit
D: DNA-dependent Protein Kinase Catalytic Subunit
E: DNA-dependent Protein Kinase Catalytic Subunit
F: DNA-dependent Protein Kinase Catalytic Subunit
X: DNA-dependent Protein Kinase Catalytic Subunit


Theoretical massNumber of molelcules
Total (without water)2,459,4037
Polymers2,459,4037
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
O: DNA-dependent Protein Kinase Catalytic Subunit
P: DNA-dependent Protein Kinase Catalytic Subunit
Q: DNA-dependent Protein Kinase Catalytic Subunit
R: DNA-dependent Protein Kinase Catalytic Subunit
S: DNA-dependent Protein Kinase Catalytic Subunit
T: DNA-dependent Protein Kinase Catalytic Subunit
Y: DNA-dependent Protein Kinase Catalytic Subunit


Theoretical massNumber of molelcules
Total (without water)2,459,4037
Polymers2,459,4037
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)168.60, 132.99, 297.00
Angle α, β, γ (deg.)90.00, 105.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DNA-dependent Protein Kinase Catalytic Subunit / DNA-PK catalytic subunit / DNA-PKcs / DNPK1 / p460


Mass: 351343.344 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Details: nuclear extracts / Source: (natural) Homo sapiens (human) / Cell line: HeLa cells S3 / References: non-specific serine/threonine protein kinase
Sequence details1. BECAUSE OF THE LOW RESOLUTION OF THE DIFFRACTION DATA, AUTHOR COULD NOT IDENTIFY THE CORRECT ...1. BECAUSE OF THE LOW RESOLUTION OF THE DIFFRACTION DATA, AUTHOR COULD NOT IDENTIFY THE CORRECT NUMBERING/TYPE OF THE RESIDUES. RESIDUE NUMBERING IS ARBITRARY, NOT CORRESPONDING TO THE ONE IN UNIPROT ENTRY, P78527. THE FOLLOWING IS THE ONE-LETTER SEQUENCE FOR THE PROTEIN MODELED IN THIS STRUCTURE, UNIPROTKB/SWISS-PROT P78527 (PRKDC_HUMAN) MAGSGAGVRCSLLRLQETLSAADRCGAALAGHQLIRGLGQECVLSSSPAVLALQTSLVFS RDFGLLVFVRKSLNSIEFRECREEILKFLCIFLEKMGQKIAPYSVEIKNTCTSVYTKDRA AKCKIPALDLLIKLLQTFRSSRLMDEFKIGELFSKFYGELALKKKIPDTVLEKVYELLGL LGEVHPSEMINNAENLFRAFLGELKTQMTSAVREPKLPVLAGCLKGLSSLLCNFTKSMEE DPQTSREIFNFVLKAIRPQIDLKRYAVPSAGLRLFALHASQFSTCLLDNYVSLFEVLLKW CAHTNVELKKAALSALESFLKQVSNMVAKNAEMHKNKLQYFMEQFYGIIRNVDSNNKELS IAIRGYGLFAGPCKVINAKDVDFMYVELIQRCKQMFLTQTDTGDDRVYQMPSFLQSVASV LLYLDTVPEVYTPVLEHLVVMQIDSFPQYSPKMQLVCCRAIVKVFLALAAKGPVLRNCIS TVVHQGLIRICSKPVVLPKGPESESEDHRASGEVRTGKWKVPTYKDYVDLFRHLLSSDQM MDSILADEAFFSVNSSSESLNHLLYDEFVKSVLKIVEKLDLTLEIQTVGEQENGDEAPGV WMIPTSDPAANLHPAKPKDFSAFINLVEFCREILPEKQAEFFEPWVYSFSYELILQSTRL PLISGFYKLLSITVRNAKKIKYFEGVSPKSLKHSPEDPEKYSCFALFVKFGKEVAVKMKQ YKDELLASCLTFLLSLPHNIIELDVRAYVPALQMAFKLGLSYTPLAEVGLNALEEWSIYI DRHVMQPYYKDILPCLDGYLKTSALSDETKNNWEVSALSRAAQKGFNKVVLKHLKKTKNL SSNEAISLEEIRIRVVQMLGSLGGQINKNLLTVTSSDEMMKSYVAWDREKRLSFAVPFRE MKPVIFLDVFLPRVTELALTASDRQTKVAACELLHSMVMFMLGKATQMPEGGQGAPPMYQ LYKRTFPVLLRLACDVDQVTRQLYEPLVMQLIHWFTNNKKFESQDTVALLEAILDGIVDP VDSTLRDFCGRCIREFLKWSIKQITPQQQEKSPVNTKSLFKRLYSLALHPNAFKRLGASL AFNNIYREFREEESLVEQFVFEALVIYMESLALAHADEKSLGTIQQCCDAIDHLCRIIEK KHVSLNKAKKRRLPRGFPPSASLCLLDLVKWLLAHCGRPQTECRHKSIELFYKFVPLLPG NRSPNLWLKDVLKEEGVSFLINTFEGGGCGQPSGILAQPTLLYLRGPFSLQATLCWLDLL LAALECYNTFIGERTVGALQVLGTEAQSSLLKAVAFFLESIAMHDIIAAEKCFGTGAAGN RTSPQEGERYNYSKCTVVVRIMEFTTTLLNTSPEGWKLLKKDLCNTHLMRVLVQTLCEPA SIGFNIGDVQVMAHLPDVCVNLMKALKMSPYKDILETHLREKITAQSIEELCAVNLYGPD AQVDRSRLAAVVSACKQLHRAGLLHNILPSQSTDLHHSVGTELLSLVYKGIAPGDERQCL PSLDLSCKQLASGLLELAFAFGGLCERLVSLLLNPAVLSTASLGSSQGSVIHFSHGEYFY SLFSETINTELLKNLDLAVLELMQSSVDNTKMVSAVLNGMLDQSFRERANQKHQGLKLAT TILQHWKKCDSWWAKDSPLETKMAVLALLAKILQIDSSVSFNTSHGSFPEVFTTYISLLA DTKLDLHLKGQAVTLLPFFTSLTGGSLEELRRVLEQLIVAHFPMQSREFPPGTPRFNNYV DCMKKFLDALELSQSPMLLELMTEVLCREQQHVMEELFQSSFRRIARRGSCVTQVGLLES VYEMFRKDDPRLSFTRQSFVDRSLLTLLWHCSLDALREFFSTIVVDAIDVLKSRFTKLNE STFDTQITKKMGYYKILDVMYSRLPKDDVHAKESKINQVFHGSCITEGNELTKTLIKLCY DAFTENMAGENQLLERRRLYHCAAYNCAISVICCVFNELKFYQGFLFSEKPEKNLLIFEN LIDLKRRYNFPVEVEVPMERKKKYIEIRKEAREAANGDSDGPSYMSSLSYLADSTLSEEM SQFDFSTGVQSYSYSSQDPRPATGRFRRREQRDPTVHDDVLELEMDELNRHECMAPLTAL VKHMHRSLGPPQGEEDSVPRDLPSWMKFLHGKLGNPIVPLNIRLFLAKLVINTEEVFRPY AKHWLSPLLQLAASENNGGEGIHYMVVEIVATILSWTGLATPTGVPKDEVLANRLLNFLM KHVFHPKRAVFRHNLEIIKTLVECWKDCLSIPYRLIFEKFSGKDPNSKDNSVGIQLLGIV MANDLPPYDPQCGIQSSEYFQALVNNMSFVRYKEVYAAAAEVLGLILRYVMERKNILEES LCELVAKQLKQHQNTMEDKFIVCLNKVTKSFPPLADRFMNAVFFLLPKFHGVLKTLCLEV VLCRVEGMTELYFQLKSKDFVQVMRHRDDERQKVCLDIIYKMMPKLKPVELRELLNPVVE FVSHPSTTCREQMYNILMWIHDNYRDPESETDNDSQEIFKLAKDVLIQGLIDENPGLQLI IRNFWSHETRLPSNTLDRLLALNSLYSPKIEVHFLSLATNFLLEMTSMSPDYPNPMFEHP LSECEFQEYTIDSDWRFRSTVLTPMFVETQASQGTLQTRTQEGSLSARWPVAGQIRATQQ QHDFTLTQTADGRSSFDWLTGSSTDPLVDHTSPSSDSLLFAHKRSERLQRAPLKSVGPDF GKKRLGLPGDEVDNKVKGAAGRTDLLRLRRRFMRDQEKLSLMYARKGVAEQKREKEIKSE LKMKQDAQVVLYRSYRHGDLPDIQIKHSSLITPLQAVAQRDPIIAKQLFSSLFSGILKEM DKFKTLSEKNNITQKLLQDFNRFLNTTFSFFPPFVSCIQDISCQHAALLSLDPAAVSAGC LASLQQPVGIRLLEEALLRLLPAELPAKRVRGKARLPPDVLRWVELAKLYRSIGEYDVLR GIFTSEIGTKQITQSALLAEARSDYSEAAKQYDEALNKQDWVDGEPTEAEKDFWELASLD CYNHLAEWKSLEYCSTASIDSENPPDLNKIWSEPFYQETYLPYMIRSKLKLLLQGEADQS LLTFIDKAMHGELQKAILELHYSQELSLLYLLQDDVDRAKYYIQNGIQSFMQNYSSIDVL LHQSRLTKLQSVQALTEIQEFISFISKQGNLSSQVPLKRLLNTWTNRYPDAKMDPMNIWD DIITNRCFFLSKIEEKLTPLPEDNSMNVDQDGDPSDRMEVQEQEEDISSLIRSCKFSMKM KMIDSARKQNNFSLAMKLLKELHKESKTRDDWLVSWVQSYCRLSHCRSRSQGCSEQVLTV LKTVSLLDENNVSSYLSKNILAFRDQNILLGTTYRIIANALSSEPACLAEIEEDKARRIL ELSGSSSEDSEKVIAGLYQRAFQHLSEAVQAAEEEAQPPSWSCGPAAGVIDAYMTLADFC DQQLRKEEENASVIDSAELQAYPALVVEKMLKALKLNSNEARLKFPRLLQIIERYPEETL SLMTKEISSVPCWQFISWISHMVALLDKDQAVAVQHSVEEITDNYPQAIVYPFIISSESY SFKDTSTGHKNKEFVARIKSKLDQGGVIQDFINALDQLSNPELLFKDWSNDVRAELAKTP VNKKNIEKMYERMYAALGDPKAPGLGAFRRKFIQTFGKEFDKHFGKGGSKLLRMKLSDFN DITNMLLLKMNKDSKPPGNLKECSPWMSDFKVEFLRNELEIPGQYDGRGKPLPEYHVRIA GFDERVTVMASLRRPKRIIIRGHDEREHPFLVKGGEDLRQDQRVEQLFQVMNGILAQDSA CSQRALQLRTYSVVPMTSRLGLIEWLENTVTLKDLLLNTMSQEEKAAYLSDPRAPPCEYK DWLTKMSGKHDVGAYMLMYKGANRTETVTSFRKRESKVPADLLKRAFVRMSTSPEAFLAL RSHFASSHALICISHWILGIGDRHLNNFMVAMETGGVIGIDFGHAFGSATQFLPVPELMP FRLTRQFINLMLPMKETGLMYSIMVHALRAFRSDPGLLTNTMDVFVKEPSFDWKNFEQKM LKKGGSWIQEINVAEKNWYPRQKICYAKRKLAGANPAVITCDELLLGHEKAPAFRDYVAV ARGSKDHNIRAQEPESGLSEETQVKCLMDQATDPNILGRTWEGWEPWM 2. THERE WAS ANOTHER ENTITY WHICH PRESENTED IN THE CRYSTAL, BUT COULD NOT BE IDENTIFIED IN THE STRUCTURE. THE ENTITY WAS GENITICALLY MANIPULATED IN E.COLI BL21(DE3), USING PLASMID PGAT3. THE ONE-LETTER SEQUENCE FOR THE ENTITY IS: UNP RESIDUES 539-732 OF UNIPROTKB/SWISS-PROT P13010 (KU86_HUMAN). LIEAKKKDQVTAQEIFQDNHEDGPTAKKLKTEQGGAHFSVSSLAEGSVTSVGSVNPAENF RVLVKQKKASFEEASNQLINHIEQFLDTNETPYFMKSIDCIRAFREEAIKFSEEQRFNNF LKALQEKVEIKQLNHFWEIVVQDGITLITKEEASGSSVTAEEAKKFLAPKDKPSGDTAAV FEEGGDVDDLLDMI

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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: 3.27 Å3/Da / Density % sol: 62.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 8% PEG 8000, 0.2M NaCl, 0.05M DTT, 0.1M Bis-Tris, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.2549, 1.2552
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 29, 2007
RadiationMonochromator: Si(311) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.25491
21.25521
ReflectionResolution: 6.6→100 Å / Num. all: 23200 / Num. obs: 22653 / % possible obs: 97.6 % / Observed criterion σ(I): 2.5 / Redundancy: 3.2 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077
Reflection shellResolution: 6.6→6.75 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.55 / Num. unique all: 1756 / Rsym value: 0.55 / % possible all: 97.3

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIX1.24.1bmodel building
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.24.1bphasing
RefinementMethod to determine structure: MAD / Resolution: 6.6→100 Å / Cor.coef. Fo:Fc: 0.626 / Cor.coef. Fo:Fc free: 0.612 / SU B: 0.008 / SU ML: 0 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / ESU R: 2.826 / ESU R Free: 2.821 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.441 1223 5.1 %RANDOM
Rwork0.442 ---
obs0.442 22653 97.64 %-
all-23200 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 80.021 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20 Å2-0.04 Å2
2--1.07 Å2-0 Å2
3----1.63 Å2
Refinement stepCycle: LAST / Resolution: 6.6→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20320 0 0 0 20320
LS refinement shellResolution: 6.6→6.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.569 96 -
Rwork0.522 1660 -
obs-1756 97.34 %

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