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- PDB-4r1f: Re-refined Human DNA topoisomerase IIa (ATPase and transducer dom... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4r1f | ||||||
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Title | Re-refined Human DNA topoisomerase IIa (ATPase and transducer domains) in complex with ADP and SO4 | ||||||
![]() | DNA topoisomerase 2-alpha | ||||||
![]() | ISOMERASE / Human topoisomerase IIA | ||||||
Function / homology | ![]() negative regulation of DNA duplex unwinding / positive regulation of single stranded viral RNA replication via double stranded DNA intermediate / sister chromatid segregation / apoptotic chromosome condensation / resolution of meiotic recombination intermediates / female meiotic nuclear division / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / embryonic cleavage / DNA ligation / Transcription of E2F targets under negative control by DREAM complex ...negative regulation of DNA duplex unwinding / positive regulation of single stranded viral RNA replication via double stranded DNA intermediate / sister chromatid segregation / apoptotic chromosome condensation / resolution of meiotic recombination intermediates / female meiotic nuclear division / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / embryonic cleavage / DNA ligation / Transcription of E2F targets under negative control by DREAM complex / DNA binding, bending / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / SUMOylation of DNA replication proteins / chromosome, centromeric region / ATP-dependent activity, acting on DNA / hematopoietic progenitor cell differentiation / condensed chromosome / ubiquitin binding / male germ cell nucleus / chromosome segregation / protein kinase C binding / regulation of circadian rhythm / rhythmic process / ribonucleoprotein complex / positive regulation of apoptotic process / protein heterodimerization activity / DNA damage response / chromatin binding / nucleolus / magnesium ion binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Stanger, F.V. / Schirmer, T. | ||||||
![]() | ![]() Title: Structure of the N-Terminal Gyrase B Fragment in Complex with ADPPi Reveals Rigid-Body Motion Induced by ATP Hydrolysis Authors: Stanger, F.V. / Dehio, C. / Schirmer, T. #1: ![]() Title: NUCLEOTIDE-DEPENDENT DOMAIN MOVEMENT in THE ATPASE DOMAIN of A HUMAN TYPE IIA DNA TOPOISOMERASE Authors: Wei, H. / Ruthenburg, A.J. / Bechis, S.K. / Verdine, G.L. | ||||||
History |
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Remark 0 | THIS ENTRY 4R1F REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R1ZXNSF) ...THIS ENTRY 4R1F REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R1ZXNSF) DETERMINED BY AUTHORS OF THE PDB ENTRY 1ZXN: AUTHOR INITIALS, AUTHOR LAST NAME |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 315.4 KB | Display | ![]() |
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PDB format | ![]() | 255.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4prvC ![]() 4prxC ![]() 4pu9C ![]() 1zxnS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: _
NCS ensembles :
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 45660.535 Da / Num. of mol.: 4 / Fragment: UNP residues 29-428 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 146 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-ADP / #4: Chemical | ChemComp-GOL / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.85 % / Description: AUTHORS USED SF DATA FROM THE ENTRY 1ZXN. |
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-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 1ZXN Resolution: 2.51→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.929 / SU B: 10.968 / SU ML: 0.236 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.733 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 186.07 Å2 / Biso mean: 64.255 Å2 / Biso min: 32.38 Å2
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Refinement step | Cycle: LAST / Resolution: 2.51→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.51→2.576 Å / Total num. of bins used: 20
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