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Yorodumi- PDB-1gxu: Hydrogenase Maturation Protein HypF "acylphosphatase-like" N-term... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gxu | ||||||
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Title | Hydrogenase Maturation Protein HypF "acylphosphatase-like" N-terminal domain (HypF-ACP) in complex with a substrate. Crystal grown in the presence of carbamoylphosphate | ||||||
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 / OTHER / 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 | 1gxu.cif.gz | 28.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gxu.ent.gz | 22.2 KB | Display | PDB format |
PDBx/mmJSON format | 1gxu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gxu_validation.pdf.gz | 413.7 KB | Display | wwPDB validaton report |
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Full document | 1gxu_full_validation.pdf.gz | 414.5 KB | Display | |
Data in XML | 1gxu_validation.xml.gz | 4.4 KB | Display | |
Data in CIF | 1gxu_validation.cif.gz | 6.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/1gxu ftp://data.pdbj.org/pub/pdb/validation_reports/gx/1gxu | 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: 10404.901 Da / Num. of mol.: 1 / Fragment: ACYLPHOSPHATASE-LIKE DOMAIN, RESIDUES 1-91 / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI (E. coli) / References: UniProt: P30131 |
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#2: Chemical | ChemComp-2HP / |
#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: 2.51 Å3/Da / Density % sol: 50.9 % | ||||||||||||||||||||||||||||||
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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: ELETTRA / Beamline: 5.2R / Wavelength: 1 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.27→30 Å / Num. obs: 27134 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 10.8 % / Rmerge(I) obs: 0.027 / Net I/σ(I): 35.7 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 292257 |
Reflection shell | *PLUS Mean I/σ(I) obs: 35.7 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 1.27→10 Å / SU B: 0.595 / SU ML: 0.029 / ESU R Free: 0.038 Details: IN THE ACTIVE SITE, WE ARE ABLE TO SEE ONLY THE PHOSPHATE MOIETY OF CARBAMOYLPHOSPHATE
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Displacement parameters | Biso mean: 17.3 Å2
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Refinement step | Cycle: LAST / Resolution: 1.27→10 Å
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Refinement | *PLUS Lowest resolution: 10 Å / Rfactor Rfree: 0.1613 / Rfactor Rwork: 0.1315 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.271 Å / Lowest resolution: 1.303 Å / Rfactor Rfree: 0.203 / Rfactor Rwork: 0.212 / Num. reflection Rwork: 1856 / Total num. of bins used: 20 |