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Yorodumi- PDB-6czp: 2.2 Angstrom Resolution Crystal Structure Oxygen-Insensitive NAD(... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 6czp | ||||||
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| Title | 2.2 Angstrom Resolution Crystal Structure Oxygen-Insensitive NAD(P)H-dependent Nitroreductase NfsB from Vibrio vulnificus in Complex with FMN | ||||||
Components | Oxygen-insensitive NAD(P)H nitroreductase | ||||||
Keywords | OXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / oxygen-insensitive nitroreductase | ||||||
| Function / homology | Function and homology information | ||||||
| Biological species | Vibrio vulnificus (bacteria) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å | ||||||
Authors | Minasov, G. / Wawrzak, Z. / Skarina, T. / Grimshaw, S. / Kwon, K. / Savchenko, A. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: Microbiol Resour Announc / Year: 2025Title: Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria. Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / ...Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / Joachimiak, A. / Anderson, W.F. / Satchell, K.J.F. | ||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 6czp.cif.gz | 711.7 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb6czp.ent.gz | 591.9 KB | Display | PDB format |
| PDBx/mmJSON format | 6czp.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/6czp ftp://data.pdbj.org/pub/pdb/validation_reports/cz/6czp | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 5tr3C ![]() 5tv2C ![]() 5ty0C ![]() 5u1oC ![]() 5u2gC ![]() 5u47C ![]() 5ue1C ![]() 5umeC ![]() 5umgC ![]() 5us8C ![]() 5uswC ![]() 5usxC ![]() 5utxC ![]() 5uu6C ![]() 5uwyC ![]() 5ux9C ![]() 5v0iC ![]() 5v36C ![]() 5vdnC ![]() 5vfbC ![]() 5vh6C ![]() 5vt3C ![]() 5wi5C ![]() 5wp0C ![]() 6aonC ![]() 6aooC ![]() 6awaC ![]() 6aziC ![]() 6b4oC ![]() 6b5fC ![]() 6b8dC ![]() 6balC ![]() 6bk7C ![]() 6blbC ![]() 6bq9C ![]() 6bz0C ![]() 6c8qC ![]() 6cmzC ![]() 6cn1C ![]() 6e5yC ![]() 6muqC ![]() 6n0iC ![]() 6n7fC ![]() 6nbkC ![]() 6nfpC ![]() 6nkjC ![]() 6po4C ![]() 6pu9C ![]() 6puaC ![]() 6pxaC ![]() 6w2zC ![]() 9bznC ![]() 9bzqC ![]() 9bzrC ![]() 1icrS S: Starting model for refinement C: citing same article ( |
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| Similar structure data | |
| Other databases |
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Links
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Assembly
| Deposited unit | ![]()
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| 3 | ![]()
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| 4 | ![]()
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| Unit cell |
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Components
-Protein , 1 types, 8 molecules ABCDEFGH
| #1: Protein | Mass: 24481.701 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio vulnificus (bacteria) / Gene: FORC36_4330 / Plasmid: pMCSG53 / Production host: ![]() |
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-Non-polymers , 6 types, 647 molecules 










| #2: Chemical | ChemComp-FMN / #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
| Has protein modification | N |
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-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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Sample preparation
| Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.8 % |
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| Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Protein: 17.0 mg/ml, 0.3M Sodium chloride, 0.01M HEPES pH 7.5, Screen: 0.2M Magnesium chloride, 0.1M Tris pH 8.5, 25% (w/v) PEG3350, Cryo: paratone |
-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
| Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 14, 2018 / Details: C(111) |
| Radiation | Monochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
| Reflection | Resolution: 2.2→30 Å / Num. obs: 88464 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 48.5 Å2 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.048 / Rrim(I) all: 0.138 / Rsym value: 0.129 / Χ2: 1.02 / Net I/σ(I): 38.3 |
| Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.768 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 4360 / CC1/2: 0.852 / Rpim(I) all: 0.3 / Rrim(I) all: 0.826 / Rsym value: 0.768 / Χ2: 1.025 / % possible all: 100 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: 1ICR Resolution: 2.24→29.91 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 12.513 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.311 / ESU R Free: 0.215 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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| Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 49.134 Å2
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| Refinement step | Cycle: 1 / Resolution: 2.24→29.91 Å
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| Refine LS restraints |
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About Yorodumi



Vibrio vulnificus (bacteria)
X-RAY DIFFRACTION
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