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Yorodumi- PDB-4utp: Crystal structure of pneumococcal surface antigen PsaA in the Cd-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4utp | ||||||
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Title | Crystal structure of pneumococcal surface antigen PsaA in the Cd- bound, closed state | ||||||
Components | MANGANESE ABC TRANSPORTER SUBSTRATE-BINDING LIPOPROTEIN | ||||||
Keywords | METAL BINDING PROTEIN / ATP BINDING / CASSETTE TRANSPORTER | ||||||
Function / homology | Function and homology information metal ion transport / cell adhesion / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | STREPTOCOCCUS PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Luo, Z. / Counago, R.M. / Maher, M. / Kobe, B. | ||||||
Citation | Journal: Nat Commun / Year: 2015 Title: Dysregulation of transition metal ion homeostasis is the molecular basis for cadmium toxicity in Streptococcus pneumoniae. Authors: Begg, S.L. / Eijkelkamp, B.A. / Luo, Z. / Counago, R.M. / Morey, J.R. / Maher, M.J. / Ong, C.L. / McEwan, A.G. / Kobe, B. / O'Mara, M.L. / Paton, J.C. / McDevitt, C.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4utp.cif.gz | 128.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4utp.ent.gz | 100.3 KB | Display | PDB format |
PDBx/mmJSON format | 4utp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4utp_validation.pdf.gz | 431.7 KB | Display | wwPDB validaton report |
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Full document | 4utp_full_validation.pdf.gz | 433 KB | Display | |
Data in XML | 4utp_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 4utp_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ut/4utp ftp://data.pdbj.org/pub/pdb/validation_reports/ut/4utp | HTTPS FTP |
-Related structure data
Related structure data | 4utoC 1pszS C: citing same article (ref.) 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: 35233.922 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A4G2 #2: Chemical | ChemComp-CD / #3: Water | ChemComp-HOH / | Sequence details | THE LAST FIVE RESIDUES GNLYF ARE THE REMAINDER OF THE HIS- TAG CLEAVAGE SITE. | |
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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: 2.37 Å3/Da / Density % sol: 48.2 % / Description: NONE |
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Crystal grow | pH: 8 Details: 26-36 % PEG 400, 0.1 M NACL, 0.1 M TRIZMA-HCL PH 8.0 AND 0.1 M CDCL2 |
-Data collection
Diffraction | Mean temperature: 193 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 2→43 Å / Num. obs: 36157 / % possible obs: 93.8 % / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.24 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 3.13 / % possible all: 93.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PSZ Resolution: 2→42.97 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.059 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.042 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.319 Å2
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Refinement step | Cycle: LAST / Resolution: 2→42.97 Å
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Refine LS restraints |
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