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Yorodumi- PDB-4fdy: Crystal structure of a similar to lipoprotein, NLP/P60 family (SA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fdy | ||||||
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Title | Crystal structure of a similar to lipoprotein, NLP/P60 family (SAV0400) from Staphylococcus aureus subsp. aureus Mu50 at 2.23 A resolution | ||||||
Components | Similar to lipoprotein, NLP/P60 family | ||||||
Keywords | HYDROLASE / Slt/lysozyme-like muramidase / NlpC/P60 LD endopeptidase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | Function and homology information Lysozyme-like / Endopeptidase, NLPC/P60 domain / NlpC/P60 family / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Lysozyme - #10 / Papain-like cysteine peptidase superfamily / Lysozyme / Lysozyme-like domain superfamily / Alpha-Beta Complex ...Lysozyme-like / Endopeptidase, NLPC/P60 domain / NlpC/P60 family / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Lysozyme - #10 / Papain-like cysteine peptidase superfamily / Lysozyme / Lysozyme-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Staphylococcus aureus subsp. aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.23 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2014 Title: Structures of a Bifunctional Cell Wall Hydrolase CwlT Containing a Novel Bacterial Lysozyme and an NlpC/P60 dl-Endopeptidase. Authors: Xu, Q. / Chiu, H.J. / Farr, C.L. / Jaroszewski, L. / Knuth, M.W. / Miller, M.D. / Lesley, S.A. / Godzik, A. / Elsliger, M.A. / Deacon, A.M. / Wilson, I.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fdy.cif.gz | 247.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fdy.ent.gz | 205.4 KB | Display | PDB format |
PDBx/mmJSON format | 4fdy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/4fdy ftp://data.pdbj.org/pub/pdb/validation_reports/fd/4fdy | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34995.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria) Strain: Mu50 / Gene: SAV0400 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q932I6, UniProt: A0A0H3JPP0*PLUS #2: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT (29-340) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (29-340) WAS EXPRESSED WITH A PURIFICATI | |
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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: 2.6 Å3/Da / Density % sol: 52.67 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.2M calcium acetate, 20.0% polyethylene glycol 8000, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97895,0.91837,0.97853 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 5, 2012 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.23→47.035 Å / Num. obs: 33428 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 53.501 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 12.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.23→47.035 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.9368 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 5. THE DENSITY FOR THE N-TERMINUS OF B CHAIN (46-71) IS POOR, THE MODEL FOR THIS REGION IS BASED ON A CHAIN.
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Displacement parameters | Biso max: 168.04 Å2 / Biso mean: 65.5059 Å2 / Biso min: 32.07 Å2
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Refine analyze | Luzzati coordinate error obs: 0.408 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.23→47.035 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.23→2.3 Å / Total num. of bins used: 17
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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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