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Yorodumi- PDB-1mwq: Structure of HI0828, a Hypothetical Protein from Haemophilus infl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mwq | ||||||
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Title | Structure of HI0828, a Hypothetical Protein from Haemophilus influenzae with a Putative Active-Site Phosphohistidine | ||||||
Components | HYPOTHETICAL PROTEIN HI0828 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / HI0828 / YCII_HAEIN / hypothetical protein / Structure 2 Function Project / S2F | ||||||
Function / homology | Function and homology information YCII-related / YCII-related domain / Dimeric alpha+beta barrel / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 0.99 Å | ||||||
Authors | Willis, M.A. / Krajewski, W. / Chalamasetty, V.R. / Reddy, P. / Howard, A. / Herzberg, O. / Structure 2 Function Project (S2F) | ||||||
Citation | Journal: Proteins / Year: 2005 Title: Structure of YciI from Haemophilus influenzae (HI0828) reveals a ferredoxin-like alpha/beta-fold with a histidine/aspartate centered catalytic site Authors: Willis, M.A. / Song, F. / Zhuang, Z. / Krajewski, W. / Chalamasetty, V.R. / Reddy, P. / Howard, A. / Dunaway-Mariano, D. / Herzberg, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mwq.cif.gz | 111.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mwq.ent.gz | 90.4 KB | Display | PDB format |
PDBx/mmJSON format | 1mwq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mwq_validation.pdf.gz | 465.4 KB | Display | wwPDB validaton report |
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Full document | 1mwq_full_validation.pdf.gz | 470.6 KB | Display | |
Data in XML | 1mwq_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 1mwq_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mw/1mwq ftp://data.pdbj.org/pub/pdb/validation_reports/mw/1mwq | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | Dynamic Light Scattering (DLS) indicates the protein is a dimer in solution. There is one dimer in the asymmetric unit. |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 11305.550 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P44887 |
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-Non-polymers , 6 types, 342 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-CAC / | #5: Chemical | ChemComp-1PE / | #6: Chemical | ChemComp-PEG / | #7: Water | ChemComp-HOH / | |
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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 Å3/Da / Density % sol: 45.19 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG4000, sodium cacodylate, sodium chloride, zinc acetate, dioxane, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
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: APS / Beamline: 17-ID / Wavelength: 0.9793, 0.9795, 0.9664, 0.9832 | |||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 23, 2001 | |||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 0.99→19.45 Å / Num. all: 206507 / Num. obs: 206417 / % possible obs: 94.2 % / Observed criterion σ(I): 0 / Redundancy: 4.76 % / Rsym value: 0.063 / Net I/σ(I): 16.7 | |||||||||||||||
Reflection shell | Resolution: 0.99→1 Å / Redundancy: 0.87 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 3599 / Rsym value: 0.3486 / % possible all: 55.7 | |||||||||||||||
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 1042859 / Rmerge(I) obs: 0.063 | |||||||||||||||
Reflection shell | *PLUS Lowest resolution: 1.1 Å / % possible obs: 83.4 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 0.99→15 Å / Num. parameters: 18707 / Num. restraintsaints: 23309 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 25 / Occupancy sum hydrogen: 1497 / Occupancy sum non hydrogen: 1916.09 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.99→15 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 15 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.132 / Rfactor Rwork: 0.109 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |