+Open data
-Basic information
Entry | Database: PDB / ID: 7nyp | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | monomeric acetyl-CoA synthase in closed conformation | |||||||||
Components | CO-methylating acetyl-CoA synthase | |||||||||
Keywords | OXIDOREDUCTASE / metalloprotein / nickel / acetogenesis / cluster A / ACS | |||||||||
Function / homology | Function and homology information CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / : / acetyl-CoA metabolic process / 4 iron, 4 sulfur cluster binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Carboxydothermus hydrogenoformans Z-2901 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Kreibich, J. / Jeoung, J.H. / Dobbek, H. | |||||||||
Funding support | Germany, 2items
| |||||||||
Citation | Journal: To Be Published Title: Ligand binding at the Ni,Ni-[4Fe-4S] cluster of acetyl-CoA synthase Authors: Kreibich, J. / Jeoung, J.H. / Dobbek, H. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7nyp.cif.gz | 579.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7nyp.ent.gz | 468.3 KB | Display | PDB format |
PDBx/mmJSON format | 7nyp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nyp_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7nyp_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 7nyp_validation.xml.gz | 63.5 KB | Display | |
Data in CIF | 7nyp_validation.cif.gz | 93 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ny/7nyp ftp://data.pdbj.org/pub/pdb/validation_reports/ny/7nyp | HTTPS FTP |
-Related structure data
Related structure data | 7nysC 7nz5C 7o0dC 1ru3S 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:
NCS oper: (Code: givenMatrix: (-0.903122381968, -0.421361284367, -0.0826113262561), (-0.418394305583, 0.90681678123, -0.0512789463184), (0.0965202996504, -0.0117470556616, -0.995261693445)Vector: -34. ...NCS oper: (Code: given Matrix: (-0.903122381968, -0.421361284367, -0.0826113262561), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 82484.570 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria) Gene: acsB, CHY_1222 / Plasmid: pQE30 Details (production host): modified vector with twinstrep-tag and TEV cleavage site Production host: Escherichia coli M15 (bacteria) References: UniProt: Q3ACS4, CO-methylating acetyl-CoA synthase |
---|
-Non-polymers , 5 types, 984 molecules
#2: Chemical | ChemComp-NI / #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.05 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop Details: 0.1 M Lithium nitrate, 16% w/v PEG 3350, 5 mM Ti(III)citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→46.44 Å / Num. obs: 96729 / % possible obs: 98.8 % / Redundancy: 2 % / Biso Wilson estimate: 32.07 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.039 / Rrim(I) all: 0.056 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.601 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 9478 / CC1/2: 0.585 / Rpim(I) all: 0.601 / Rrim(I) all: 0.849 / % possible all: 97.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RU3 Resolution: 2.1→46.43 Å / SU ML: 0.254 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.0482 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.11 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→46.43 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.887065110097 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|