+Open data
-Basic information
Entry | Database: PDB / ID: 8vab | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of FeII/FeII CtCADD from Chlamydia trachomatis | ||||||
Components | 4-aminobenzoate synthase | ||||||
Keywords | OXIDOREDUCTASE / FeII reconstituted form | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on the CH-CH group of donors; With oxygen as acceptor / small molecule metabolic process / sulfur compound metabolic process / toxin activity / host cell cytoplasm / oxidoreductase activity / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Chlamydia trachomatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Phan, H.N. / Swartz, P.D. / Makris, T.M. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Biochemistry / Year: 2024 Title: Assembly of a Heterobimetallic Fe/Mn Cofactor in the para -Aminobenzoate Synthase Chlamydia Protein Associating with Death Domains (CADD) Initiates Long-Range Radical Hole-Hopping. Authors: Phan, H.N. / Swartz, P.D. / Gangopadhyay, M. / Guo, Y. / Smirnov, A.I. / Makris, T.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8vab.cif.gz | 65.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8vab.ent.gz | 39.7 KB | Display | PDB format |
PDBx/mmJSON format | 8vab.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vab_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8vab_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8vab_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 8vab_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/va/8vab ftp://data.pdbj.org/pub/pdb/validation_reports/va/8vab | HTTPS FTP |
-Related structure data
Related structure data | 8va9C 8vagC 8vaiC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 27769.285 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Strain: Strain D/UW-3/Cx / Gene: CT_610 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O84616 | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.3 % / Description: Hexagonal plates |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: 0.2M Lithium citrate tribasic tetrahydrate, 20% w/v PEG-3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54184 Å |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Apr 18, 2023 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54184 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→18.11 Å / Num. obs: 9563 / % possible obs: 98.04 % / Redundancy: 18.2 % / Biso Wilson estimate: 53.6 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.2071 / Rpim(I) all: 0.04942 / Rrim(I) all: 0.213 / Net I/σ(I): 8.77 |
Reflection shell | Resolution: 2.65→2.744 Å / Rmerge(I) obs: 1.008 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.912 / CC star: 0.977 / Rpim(I) all: 0.2437 / Rrim(I) all: 1.038 / % possible all: 95.61 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→18.11 Å / SU ML: 0.425 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3205 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→18.11 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|