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Yorodumi- PDB-1gxt: Hydrogenase Maturation Protein HypF "acylphosphatase-like" N-term... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gxt | ||||||
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Title | Hydrogenase Maturation Protein HypF "acylphosphatase-like" N-terminal domain (HypF-ACP) in complex with Sulfate | ||||||
Components | HYDROGENASE MATURATION PROTEIN HYPF | ||||||
Keywords | PHOSPHATASE / ACYLPHOSPHATASES / HYDROGENASE MATURATIONS / FIBRIL FORMATION / ZINC-FINGER | ||||||
Function / homology | Function and homology information Ligases; Forming carbon-sulfur bonds / carboxyl- or carbamoyltransferase activity / ATPase complex / ligase activity / protein maturation / double-stranded RNA binding / protein-containing complex assembly / zinc ion binding Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.27 Å | ||||||
Authors | Rosano, C. / Zuccotti, S. / Stefani, M. / Bucciantini, M. / Ramponi, G. / Bolognesi, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Crystal Structure and Anion Binding in the Prokaryotic Hydrogenase Maturation Factor Hypf Acylphosphatase-Like Domain Authors: Rosano, C. / Zuccotti, S. / Bucciantini, M. / Stefani, M. / Ramponi, G. / Bolognesi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gxt.cif.gz | 31.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gxt.ent.gz | 24.6 KB | Display | PDB format |
PDBx/mmJSON format | 1gxt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/1gxt ftp://data.pdbj.org/pub/pdb/validation_reports/gx/1gxt | HTTPS FTP |
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-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: 10461.952 Da / Num. of mol.: 1 / Fragment: ACYLPHOSPHATASE-LIKE DOMAIN, RESIDUES 1-91 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P30131 |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-TRS / |
#5: 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: 2.52 Å3/Da / Density % sol: 51.3 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: pH 8.50 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.5 / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8443 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8443 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→20 Å / Num. obs: 28517 / % possible obs: 92.9 % / Observed criterion σ(I): 2 / Redundancy: 10.5 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 16.3 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 299640 |
Reflection shell | *PLUS Mean I/σ(I) obs: 16.32 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.27→10 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.65 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.94 Å2
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Refinement step | Cycle: LAST / Resolution: 1.27→10 Å
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