[English] 日本語
Yorodumi- PDB-1kbv: NITRITE-SOAKED CRYSTAL STRUCTURE OF THE SOLUBLE DOMAIN OF ANIA FR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kbv | ||||||
---|---|---|---|---|---|---|---|
Title | NITRITE-SOAKED CRYSTAL STRUCTURE OF THE SOLUBLE DOMAIN OF ANIA FROM NEISSERIA GONORRHOEAE | ||||||
Components | Major outer membrane protein PAN 1 | ||||||
Keywords | OXIDOREDUCTASE / ANIA[NO2-] | ||||||
Function / homology | Function and homology information nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / ferroxidase activity / cell outer membrane / outer membrane-bounded periplasmic space / copper ion binding Similarity search - Function | ||||||
Biological species | Neisseria gonorrhoeae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Boulanger, M.J. / Murphy, M.E.P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Crystal structure of the soluble domain of the major anaerobically induced outer membrane protein (AniA) from pathogenic Neisseria: a new class of copper-containing nitrite reductases. Authors: Boulanger, M.J. / Murphy, M.E. | ||||||
History |
| ||||||
Remark 999 | SEQUENCE ACCORDING TO THE AUTHOR THE SEQUENCE DIFFERENCES EXIST BETWEEN HIS SEQUENCE AND THE ...SEQUENCE ACCORDING TO THE AUTHOR THE SEQUENCE DIFFERENCES EXIST BETWEEN HIS SEQUENCE AND THE SWISSPROT ENTRY Q02219. AUTHOR'S SEQUENCE IS IDENTICAL TO THE SEQUENCE OBTAINGED FROM THE GONOCOCCAL GENOME SEQUENCING PROJECT (A49208) SUPPORTED BY USPHS/NIH GRANT #AI38399, AND B.A.ROE, L.SONG, S.P.LIN, X.YUAN, S.CLIFTON, T.DUCEY, L.LEWIS AND D.W.DYER AT THE UNIVERSITY OF OKLAHOMA - ACGT. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1kbv.cif.gz | 397.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1kbv.ent.gz | 316.9 KB | Display | PDB format |
PDBx/mmJSON format | 1kbv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kbv_validation.pdf.gz | 493.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1kbv_full_validation.pdf.gz | 548 KB | Display | |
Data in XML | 1kbv_validation.xml.gz | 93.7 KB | Display | |
Data in CIF | 1kbv_validation.cif.gz | 135.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/1kbv ftp://data.pdbj.org/pub/pdb/validation_reports/kb/1kbv | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | The physiological molecule is the homotrimer |
-Components
#1: Protein | Mass: 35212.746 Da / Num. of mol.: 6 / Fragment: Residues 42-364, soluble domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: aniA / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: Q02219 #2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-NO2 / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.91 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10.5 Details: 1.7 M (NH4)2SO4, 0.2 M LiSO4 and 0.1 M CAPS, PH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 7 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 12, 2000 / Details: osmic mirrors |
Radiation | Monochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. all: 171343 / Num. obs: 149119 / % possible obs: 87 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.95→2.07 Å / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 6.3 / Num. unique all: 14912 / % possible all: 52.2 |
Reflection | *PLUS Lowest resolution: 50 Å / % possible obs: 87 % / Num. measured all: 697886 |
Reflection shell | *PLUS % possible obs: 52.2 % / Num. unique obs: 14912 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→49.18 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1755945.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 65.6322 Å2 / ksol: 0.368156 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.9 Å2
| ||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→49.18 Å
| ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.95→2.07 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.256 / % reflection Rfree: 10 % / Rfactor Rwork: 0.221 |