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- PDB-3zka: CRYSTAL STRUCTURE OF PNEUMOCOCCAL SURFACE ANTIGEN PSAA D280N IN T... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3zka | |||||||||
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Title | CRYSTAL STRUCTURE OF PNEUMOCOCCAL SURFACE ANTIGEN PSAA D280N IN THE METAL-BOUND, OPEN STATE | |||||||||
![]() | MANGANESE ABC TRANSPORTER SUBSTRATE-BINDING LIPOPROTEIN | |||||||||
![]() | METAL TRANSPORT / ATP-BINDING CASSETTE TRANSPORTERS / BACTERIAL ADHESION / CARRIER PROTEINS / LIPOPROTEINS / MEMBRANE TRANSPORT PROTEINS | |||||||||
Function / homology | ![]() metal ion transport / cell adhesion / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Counago, R.M. / Ween, M.P. / Bajaj, M. / Zuegg, J. / Cooper, M.A. / McEwan, A.G. / Paton, J.C. / Kobe, B. / McDevitt, C.A. | |||||||||
![]() | ![]() 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: ![]() 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: ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 446.5 KB | Display | ![]() |
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PDB format | ![]() | 368.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.8 KB | Display | ![]() |
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Full document | ![]() | 437.4 KB | Display | |
Data in XML | ![]() | 26.5 KB | Display | |
Data in CIF | ![]() | 39.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3zk7C ![]() 3zk8C ![]() 3zk9C ![]() 1pszS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (1, 0.028, -0.005), Vector: |
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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.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.31 % / Description: NONE |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 0.95369 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→22.7 Å / Num. obs: 71639 / % possible obs: 95.4 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 22.39 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.55→1.59 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.1 / % possible all: 86.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PSZ Resolution: 1.55→22.69 Å / Cor.coef. Fo:Fc: 0.9631 / Cor.coef. Fo:Fc free: 0.9527 / SU R Cruickshank DPI: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.079 / SU Rfree Blow DPI: 0.081 / SU Rfree Cruickshank DPI: 0.082 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=9429. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=9429. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=2.
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Displacement parameters | Biso mean: 28.48 Å2
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Refine analyze | Luzzati coordinate error obs: 0.194 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→22.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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