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Yorodumi- PDB-1hq0: CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF E.COLI CYTOTOXIC NEC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hq0 | ||||||
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Title | CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF E.COLI CYTOTOXIC NECROTIZING FACTOR TYPE 1 | ||||||
Components | CYTOTOXIC NECROTIZING FACTOR 1 | ||||||
Keywords | TOXIN / BETA SANDWICH / RHO DEAMIDASE / RHO TRANSGLUTAMINASE | ||||||
Function / homology | Function and homology information Cytotoxic necrotizing factor 1 (CNF1) / Cytotoxic necrotizing factor, Rho-activating domain / Cytotoxic necrotizing factor, Rho-activating domain / Domain of unknown function DUF4765 / Cytotoxic necrotizing factor, Rho-activating domain superfamily / Rho-activating domain of cytotoxic necrotizing factor / Domain of unknown function (DUF4765) / Domain of unknown function DUF6543 / Dermonecrotic toxin, N-terminal domain / Cytotoxic necrotizing factor-like, catalytic ...Cytotoxic necrotizing factor 1 (CNF1) / Cytotoxic necrotizing factor, Rho-activating domain / Cytotoxic necrotizing factor, Rho-activating domain / Domain of unknown function DUF4765 / Cytotoxic necrotizing factor, Rho-activating domain superfamily / Rho-activating domain of cytotoxic necrotizing factor / Domain of unknown function (DUF4765) / Domain of unknown function DUF6543 / Dermonecrotic toxin, N-terminal domain / Cytotoxic necrotizing factor-like, catalytic / 4-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.83 Å | ||||||
Authors | Buetow, L. / Flatau, G. / Chiu, K. / Boquet, P. / Ghosh, P. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2001 Title: Structure of the Rho-activating domain of Escherichia coli cytotoxic necrotizing factor 1. Authors: Buetow, L. / Flatau, G. / Chiu, K. / Boquet, P. / Ghosh, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hq0.cif.gz | 74.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hq0.ent.gz | 55 KB | Display | PDB format |
PDBx/mmJSON format | 1hq0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hq0_validation.pdf.gz | 437.7 KB | Display | wwPDB validaton report |
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Full document | 1hq0_full_validation.pdf.gz | 440.5 KB | Display | |
Data in XML | 1hq0_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 1hq0_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hq/1hq0 ftp://data.pdbj.org/pub/pdb/validation_reports/hq/1hq0 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32658.438 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN / Mutation: L794P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CNF1 / Plasmid: PET 28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q47106 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.358 Å3/Da / Density % sol: 55 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 310 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Sodium phosphate, potassium phosphate, 1,4-butanediol, HEPES, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 37 ℃ / pH: 8 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.76→20 Å / Num. all: 29261 / Num. obs: 26431 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Biso Wilson estimate: 20.7 Å2 / Limit h max: 26 / Limit h min: 0 / Limit k max: 26 / Limit k min: 0 / Limit l max: 99 / Limit l min: 0 / Observed criterion F max: 1515682.95 / Observed criterion F min: 7.5 / Rmerge(I) obs: 0.056 / Net I/σ(I): 36.7 | ||||||||||||||||||
Reflection shell | Resolution: 1.76→1.81 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 2.6 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.83→20 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 52.0432 Å2 / ksol: 0.336574 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.96 Å2 / Biso mean: 28.05 Å2 / Biso min: 11.59 Å2
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Refine Biso |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.83→20 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 4.9 % / Rfactor obs: 0.191 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.262 / % reflection Rfree: 4.4 % / Rfactor Rwork: 0.247 |