[English] 日本語
Yorodumi- PDB-7zmq: Crystal structure of human RECQL5 helicase APO form in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zmq | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G2*-006 | |||||||||
Components |
| |||||||||
Keywords | HYDROLASE / Helicase / Apo form / Nanobody complex | |||||||||
Function / homology | Function and homology information mitotic DNA-templated DNA replication / chromosome separation / cellular response to camptothecin / four-way junction helicase activity / replication-born double-strand break repair via sister chromatid exchange / DNA 3'-5' helicase / transcription preinitiation complex / DNA metabolic process / negative regulation of transcription elongation by RNA polymerase II / DNA unwinding involved in DNA replication ...mitotic DNA-templated DNA replication / chromosome separation / cellular response to camptothecin / four-way junction helicase activity / replication-born double-strand break repair via sister chromatid exchange / DNA 3'-5' helicase / transcription preinitiation complex / DNA metabolic process / negative regulation of transcription elongation by RNA polymerase II / DNA unwinding involved in DNA replication / RNA polymerase II complex binding / 3'-5' DNA helicase activity / negative regulation of double-strand break repair via homologous recombination / DNA helicase activity / isomerase activity / helicase activity / replication fork / double-strand break repair via homologous recombination / cellular response to xenobiotic stimulus / chromosome / mitotic cell cycle / DNA replication / cell division / DNA repair / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Lama glama (llama) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Ye, M. / Makola, M. / Newman, J.A. / Fairhead, M. / MacLean, E. / Krojer, T. / Aitkenhead, H. / Bountra, C. / Gileadi, O. / von Delft, F. | |||||||||
Funding support | China, 1items
| |||||||||
Citation | Journal: To Be Published Title: Gluebodies improve crystal reliability and diversity through transferable nanobody mutations that introduce constitutive crystal contacts Authors: Ye, M. / Makola, M. / Newman, J.A. / Fairhead, M. / MacLean, E. / Krojer, T. / Wright, N.D. / Koekemoer, L. / Thompson, A. / Bezerra, G.A. / Yi, G. / Li, H. / Rangel, V.L. / Mamalis, D. / ...Authors: Ye, M. / Makola, M. / Newman, J.A. / Fairhead, M. / MacLean, E. / Krojer, T. / Wright, N.D. / Koekemoer, L. / Thompson, A. / Bezerra, G.A. / Yi, G. / Li, H. / Rangel, V.L. / Mamalis, D. / Aitkenhead, H. / Gilbert, R.J.C. / Duerr, K. / Davis, B.G. / Bountra, C. / Gileadi, O. / von Delft, F. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7zmq.cif.gz | 242.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7zmq.ent.gz | 185.9 KB | Display | PDB format |
PDBx/mmJSON format | 7zmq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zmq_validation.pdf.gz | 462.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7zmq_full_validation.pdf.gz | 472.2 KB | Display | |
Data in XML | 7zmq_validation.xml.gz | 39.6 KB | Display | |
Data in CIF | 7zmq_validation.cif.gz | 55.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/7zmq ftp://data.pdbj.org/pub/pdb/validation_reports/zm/7zmq | HTTPS FTP |
-Related structure data
Related structure data | 7zmlC 7zmmC 7zmnC 7zmoC 7zmpC 7zmrC 7zmsC 7zmtC 7zmvC 5lb5S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: End auth comp-ID: SER / End label comp-ID: SER
NCS ensembles :
|
-Components
#1: Protein | Mass: 49537.180 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RECQL5, RECQ5 / Production host: Escherichia coli (E. coli) / References: UniProt: O94762, DNA helicase #2: Antibody | Mass: 13803.143 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.94 Å3/Da / Density % sol: 68.79 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M lithium sulfate -- 25% PEG3350 -- 0.1M tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9119 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 17, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9119 Å / Relative weight: 1 |
Reflection | Resolution: 2.41→99.68 Å / Num. obs: 77373 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.9 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.41→2.45 Å / Num. unique obs: 3878 / CC1/2: 0.3 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LB5 Resolution: 2.7→99.665 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.903 / WRfactor Rfree: 0.233 / WRfactor Rwork: 0.203 / SU B: 12.432 / SU ML: 0.246 / Average fsc free: 0.8813 / Average fsc work: 0.8947 / Cross valid method: FREE R-VALUE / ESU R: 0.455 / ESU R Free: 0.294 Details: Hydrogens have been added in their riding positions
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.392 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→99.665 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
|