+Open data
-Basic information
Entry | Database: PDB / ID: 3myu | ||||||
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Title | Mycoplasma genitalium MG289 | ||||||
Components | High affinity transport system protein p37 | ||||||
Keywords | VIB BINDING PROTEIN / MYCOPLASMA / MYCOPLASMA GENITALIUM / MG289 / P37 / G37 / CYPL / EXTRACYTOPLASMIC / THIAMINE BINDING PROTEIN / LIPOPROTEIN / ATP BINDING CASSETTE TRANSPORTER BINDING PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycoplasma genitalium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Sippel, K.H. / Boehlein, S.K. / Govindasamy, L. / Namiki, K. / Satai, Y. / Quirit, J.G. / Agbandje-McKenna, M. / Goodison, S. / Rosser, C.J. / Sankaran, B. / McKenna, R. | ||||||
Citation | Journal: Proteins / Year: 2011 Title: Insights into Mycoplasma genitalium metabolism revealed by the structure of MG289, an extracytoplasmic thiamine binding lipoprotein. Authors: Sippel, K.H. / Venkatakrishnan, B. / Boehlein, S.K. / Sankaran, B. / Quirit, J.G. / Govindasamy, L. / Agbandje-McKenna, M. / Goodison, S. / Rosser, C.J. / McKenna, R. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2009 Title: Cloning, expression, purification, crystallization and preliminary X-ray analysis of Mycoplasma genitalium protein MG289. Authors: Sippel, K.H. / Boehlein, S.K. / Sakai, Y. / Quirit, J.G. / Agbandje-McKenna, M. / Rosser, C.J. / McKenna, R. #2: Journal: J.Bacteriol. / Year: 2009 Title: Structural insights into the extracytoplasmic thiamine-binding lipoprotein p37 of Mycoplasma hyorhinis. Authors: Sippel, K.H. / Robbins, A.H. / Reutzel, R. / Boehlein, S.K. / Namiki, K. / Goodison, S. / Agbandje-McKenna, M. / Rosser, C.J. / McKenna, R. #3: Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: Structure determination of the cancer-associated Mycoplasma hyorhinis protein Mh-p37. Authors: Sippel, K.H. / Robbins, A.H. / Reutzel, R. / Domsic, J. / Boehlein, S.K. / Govindasamy, L. / Agbandje-McKenna, M. / Rosser, C.J. / McKenna, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3myu.cif.gz | 153.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3myu.ent.gz | 119.4 KB | Display | PDB format |
PDBx/mmJSON format | 3myu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3myu_validation.pdf.gz | 981.9 KB | Display | wwPDB validaton report |
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Full document | 3myu_full_validation.pdf.gz | 992.4 KB | Display | |
Data in XML | 3myu_validation.xml.gz | 28.3 KB | Display | |
Data in CIF | 3myu_validation.cif.gz | 39.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/my/3myu ftp://data.pdbj.org/pub/pdb/validation_reports/my/3myu | HTTPS FTP |
-Related structure data
Related structure data | 3ekiS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 39552.562 Da / Num. of mol.: 2 / Fragment: N-TERMINAL TRUNCATION (DELTA 1-25) / Mutation: S26M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycoplasma genitalium (bacteria) / Strain: G37 / Gene: MG289, p37 / Plasmid: pET31f1m1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q49410 #2: Chemical | #3: Chemical | #4: 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: 2.47 Å3/Da / Density % sol: 50.16 % |
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Crystal grow | Temperature: 298 K / pH: 4.6 Details: 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM ACETATE TRIHYDRATE pH 4.6 and 15% PEG 4000 AND HAMPTON SILVER BULLET BIO CONDITION 49, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2009 Details: VERTICALLY COLLIMATING PREMIRROR, LN2 COOLED DOUBLE- CRYSTAL SILICON (111) MONOCHROMATOR, TOROIDAL FOCUSING M2 MIRROR |
Radiation | Monochromator: LIQUID NITROGEN COOLED DUAL SI(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→45.18 Å / Num. obs: 52800 / % possible obs: 90.9 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 34.6 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.56 / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3EKI Resolution: 1.95→45.18 Å / SU ML: 0.22 / σ(F): 0.11 / Phase error: 28.39 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.809 Å2 / ksol: 0.321 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→45.18 Å
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Refine LS restraints |
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LS refinement shell |
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