+Open data
-Basic information
Entry | Database: PDB / ID: 3hl6 | ||||||
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Title | Staphylococcus aureus pathogenicity island 3 ORF9 protein | ||||||
Components | Pathogenicity island protein | ||||||
Keywords | UNKNOWN FUNCTION / Staphylococcus aureus / pathogenicity island | ||||||
Function / homology | Function and homology information Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #700 / Putative mobile pathogenicity island, N-terminal domain / Putative mobile pathogenicity island / Putative mobile pathogenicity island, N-terminal domain / Putative mobile pathogenicity island / Pantoate--beta-alanine Ligase; Chain: A,domain 2 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Staphylococcus aureus subsp. aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MIRAS / Resolution: 2.5 Å | ||||||
Authors | Kruse, A.C. / Huseby, M. / Shi, K. / Digre, J. / Schlievert, P.M. / Ohlendorf, D.H. / Earhart, C.A. | ||||||
Citation | Journal: To be Published Title: Structural and functional studies of a pathogenicity island protein from Staphylococcus aureus Authors: Kruse, A.C. / Huseby, M. / Shi, K. / Digre, J. / Schlievert, P.M. / Ohlendorf, D.H. / Earhart, C.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hl6.cif.gz | 88.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hl6.ent.gz | 68.4 KB | Display | PDB format |
PDBx/mmJSON format | 3hl6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hl6_validation.pdf.gz | 443.7 KB | Display | wwPDB validaton report |
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Full document | 3hl6_full_validation.pdf.gz | 459.9 KB | Display | |
Data in XML | 3hl6_validation.xml.gz | 18 KB | Display | |
Data in CIF | 3hl6_validation.cif.gz | 23.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/3hl6 ftp://data.pdbj.org/pub/pdb/validation_reports/hl/3hl6 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25922.139 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria) Strain: COL / Gene: SACOL0900 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5HHI6, UniProt: A0A0H2WYW3*PLUS #2: Chemical | #3: 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: 2.5 Å3/Da / Density % sol: 50.78 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 3 M sodium nitrate, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 125 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 13, 2009 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 17190 / Num. obs: 17190 / % possible obs: 96.7 % / Redundancy: 3.5 % / Rsym value: 0.043 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 730 / Rsym value: 0.391 / % possible all: 83.8 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.925 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.539 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.175 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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