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- PDB-1x9n: Crystal Structure of Human DNA Ligase I bound to 5'-adenylated, n... -

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Basic information

Entry
Database: PDB / ID: 1x9n
TitleCrystal Structure of Human DNA Ligase I bound to 5'-adenylated, nicked DNA
Components
  • 5'-phosphorylated DNA
  • DNA ligase ILIG1
  • dideoxy terminated DNA
  • template DNA
KeywordsLigase/DNA / DNA ligase / 5'-adenylated nicked DNA / protein-DNA complex / Ligase-DNA COMPLEX
Function / homology
Function and homology information


Okazaki fragment processing involved in mitotic DNA replication / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / Processive synthesis on the lagging strand / DNA ligation / Processive synthesis on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / lagging strand elongation ...Okazaki fragment processing involved in mitotic DNA replication / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / Processive synthesis on the lagging strand / DNA ligation / Processive synthesis on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / lagging strand elongation / DNA biosynthetic process / Early Phase of HIV Life Cycle / PCNA-Dependent Long Patch Base Excision Repair / POLB-Dependent Long Patch Base Excision Repair / mismatch repair / anatomical structure morphogenesis / base-excision repair, gap-filling / Gap-filling DNA repair synthesis and ligation in GG-NER / base-excision repair / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA recombination / cell division / DNA repair / intracellular membrane-bounded organelle / mitochondrion / DNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus
Similarity search - Function
DNA ligase i, domain 1 / DNA ligase, ATP-dependent, N-terminal domain / Dna Ligase; domain 1 - #70 / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / ATP-dependent DNA ligase signature 2. / ATP-dependent DNA ligase AMP-binding site. / DNA ligase/mRNA capping enzyme ...DNA ligase i, domain 1 / DNA ligase, ATP-dependent, N-terminal domain / Dna Ligase; domain 1 - #70 / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / ATP-dependent DNA ligase signature 2. / ATP-dependent DNA ligase AMP-binding site. / DNA ligase/mRNA capping enzyme / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / DNA ligase, ATP-dependent, conserved site / ATP-dependent DNA ligase family profile. / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Nucleic acid-binding proteins / Dna Ligase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / DNA / DNA (> 10) / DNA ligase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsPascal, J.M. / O'Brien, P.J. / Tomkinson, A.E. / Ellenberger, T.
CitationJournal: Nature / Year: 2004
Title: Human DNA ligase I completely encircles and partially unwinds nicked DNA.
Authors: Pascal, J.M. / O'Brien, P.J. / Tomkinson, A.E. / Ellenberger, T.
History
DepositionAug 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: dideoxy terminated DNA
C: 5'-phosphorylated DNA
D: template DNA
A: DNA ligase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1105
Polymers93,7624
Non-polymers3471
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)161.889, 161.889, 88.455
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: DNA chain dideoxy terminated DNA


Mass: 3982.596 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-phosphorylated DNA


Mass: 4641.008 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain template DNA


Mass: 8529.511 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Protein DNA ligase I / LIG1 / 6.5.1.1 / Polydeoxyribonucleotide synthase [ATP]


Mass: 76609.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIG1 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RP / References: UniProt: P18858, DNA ligase (ATP)
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM

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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: 3.94 Å3/Da / Density % sol: 69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: PEG 4000, sodium acetate, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2sodium acetate11
3H2O11
4PEG 400012
5sodium acetate12
6H2O12

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONNSLS X2510.9788
SYNCHROTRONNSLS X2520.9787, 0.9791, 0.9635, 1.1
SYNCHROTRONNSLS X12C31.006, 1.011, 0.969, 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 25, 2003
RadiationMonochromator: double crystal monochromator Si(111) or (220)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97881
20.97871
30.97911
40.96351
51.11
61.0061
71.0111
80.9691
ReflectionResolution: 3→50 Å / Num. all: 26365 / Num. obs: 26365 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 10 % / Rsym value: 0.078 / Net I/σ(I): 23.1
Reflection shellResolution: 3→3.11 Å / Mean I/σ(I) obs: 5 / Rsym value: 0.48 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.1.80refinement
ACEdata reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.902 / SU B: 17.766 / SU ML: 0.311 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.209 / ESU R Free: 0.394 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26833 1301 5 %RANDOM
Rwork0.23459 ---
obs0.23626 24943 50 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.591 Å2
Baniso -1Baniso -2Baniso -3
1--3.65 Å2-1.82 Å20 Å2
2---3.65 Å20 Å2
3---5.47 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4894 813 23 0 5730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0215929
X-RAY DIFFRACTIONr_angle_refined_deg1.5242.1588207
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6035630
X-RAY DIFFRACTIONr_chiral_restr0.0830.2890
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024186
X-RAY DIFFRACTIONr_nbd_refined0.2540.22408
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3160.226
X-RAY DIFFRACTIONr_mcbond_it0.4581.53155
X-RAY DIFFRACTIONr_mcangle_it0.93825078
X-RAY DIFFRACTIONr_scbond_it1.58732773
X-RAY DIFFRACTIONr_scangle_it2.5974.53126
LS refinement shellResolution: 3→3.076 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.413 103
Rwork0.332 1811
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)
13.98951.4420.03232.07431.00912.21560.0941-0.1954-0.15160.09040.11350.42080.1322-0.0302-0.20760.36020.0338-0.19330.2820.34430.574953.808132.577964.4371
22.59080.18670.06222.2446-0.66670.95560.16890.615-0.0202-0.32740.01480.3758-0.1052-0.2482-0.18370.65170.0041-0.26270.76930.06490.486457.292740.756830.3652
35.61810.14380.42273.7920.47064.31940.01780.2943-0.0817-0.28770.06550.342-0.3951-0.3272-0.08330.43150.0622-0.34770.48720.28320.80824.342243.877540.3222
42.583-0.519-0.71110.8286-0.15363.5126-0.03630.2699-0.2147-0.3180.14970.1582-0.0001-0.1064-0.11350.4026-0.0538-0.31570.29690.19940.788440.784135.333645.906
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AD262 - 53531 - 304
2X-RAY DIFFRACTION2AD536 - 747305 - 516
3X-RAY DIFFRACTION3AD748 - 901517 - 670
4X-RAY DIFFRACTION4BA3 - 133 - 13
5X-RAY DIFFRACTION4CB1 - 91 - 9
6X-RAY DIFFRACTION4DC7 - 267 - 26
7X-RAY DIFFRACTION4CE1001

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