[English] 日本語
Yorodumi- PDB-3zk9: CRYSTAL STRUCTURE OF PNEUMOCOCCAL SURFACE ANTIGEN PSAA D280N IN T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zk9 | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF PNEUMOCOCCAL SURFACE ANTIGEN PSAA D280N IN THE METAL-FREE, OPEN STATE | ||||||
Components | MANGANESE ABC TRANSPORTER SUBSTRATE-BINDING LIPOPROTEIN | ||||||
Keywords | METAL TRANSPORT / ATP-BINDING CASSETTE TRANSPORTERS / BACTERIAL ADHESION / CARRIER PROTEINS / LIPOPROTEINS / MEMBRANE TRANSPORT PROTEINS | ||||||
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: 1.45 Å | ||||||
Authors | Counago, R.M. / Ween, M.P. / Bajaj, M. / Zuegg, J. / Cooper, M.A. / McEwan, A.G. / Paton, J.C. / Kobe, B. / McDevitt, C.A. | ||||||
Citation | Journal: Nat. Chem. Biol. / Year: 2014 Title: Imperfect coordination chemistry facilitates metal ion release in the Psa permease. Authors: Counago, R.M. / Ween, M.P. / Begg, S.L. / Bajaj, M. / Zuegg, J. / O'Mara, M.L. / Cooper, M.A. / McEwan, A.G. / Paton, J.C. / Kobe, B. / McDevitt, C.A. #1: Journal: Structure / Year: 1998 Title: The Crystal Structure of Pneumococcal Surface Antigen Psaa Reveals a Metal-Binding Site and a Novel Structure for a Putative Abc-Type Binding Protein. Authors: Lawrence, M.C. / Pilling, P.A. / Epa, V.C. / Berry, A.M. / Ogunniyi, A.D. / Paton, J.C. #2: Journal: Plos Pathog. / Year: 2011 Title: A Molecular Mechanism for Bacterial Susceptibility to Zinc. Authors: McDevitt, C.A. / Ogunniyi, A.D. / Valkov, E. / Lawrence, M.C. / Kobe, B. / McEwan, A.G. / Paton, J.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3zk9.cif.gz | 439.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3zk9.ent.gz | 364 KB | Display | PDB format |
PDBx/mmJSON format | 3zk9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/3zk9 ftp://data.pdbj.org/pub/pdb/validation_reports/zk/3zk9 | HTTPS FTP |
---|
-Related structure data
Related structure data | 3zk7C 3zk8C 3zkaC 1pszS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.997, 0.082, 0.014), Vector: |
-Components
#1: Protein | Mass: 31444.402 Da / Num. of mol.: 2 / Fragment: RESIDUES 32-309 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A4G2 #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.31 % / Description: NONE |
---|---|
Crystal grow | Temperature: 293 K Details: 12.5% W/V PEG 1,000 12.5% W/V PEG 3,350, 12.5% V/V MPD; 0.1 M TRIZMA/BICINE PH 8.7 AFTER 7-10 DAYS AT 293 K, FOLLOWING STREAK-SEEDING OF PRE-EQUILIBRATED (24 HOURS) DROPS. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 |
Detector | Type: ADSC CCD / Detector: CCD / Details: SILICON MIRRORS (ADAPTIVE AND U-BENT) |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR (SI111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→19.46 Å / Num. obs: 91166 / % possible obs: 95.5 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 15.97 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 1.45→1.47 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 4.8 / % possible all: 85.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PSZ Resolution: 1.45→19.46 Å / Cor.coef. Fo:Fc: 0.9687 / Cor.coef. Fo:Fc free: 0.9594 / SU R Cruickshank DPI: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.057 / SU Rfree Blow DPI: 0.059 / SU Rfree Cruickshank DPI: 0.059 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.42 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.128 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→19.46 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.45→1.49 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|