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Yorodumi- PDB-4q68: Crystal structure of a N-acetylmuramoyl-L-alanine amidase (BACUNI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4q68 | ||||||
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Title | Crystal structure of a N-acetylmuramoyl-L-alanine amidase (BACUNI_02947) from Bacteroides uniformis ATCC 8492 at 1.07 A resolution | ||||||
Components | Uncharacterized protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF07313 family protein / DUF 1460 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | Function and homology information Putative xylanase fold / Putative xylanase like domain / putative xylanase like fold / putative xylanase like domain / N-acetylmuramoyl-L-alanine amidase-like / N-acetylmuramoyl-L-alanine amidase-like / Papain-like cysteine peptidase superfamily / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | Bacteroides uniformis ATCC 8492 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: Structure / Year: 2014 Title: Structure-guided functional characterization of DUF1460 reveals a highly specific NlpC/P60 amidase family. Authors: Xu, Q. / Mengin-Lecreulx, D. / Patin, D. / Grant, J.C. / Chiu, H.J. / Jaroszewski, L. / Knuth, M.W. / Godzik, A. / Lesley, S.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 | 4q68.cif.gz | 143.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q68.ent.gz | 110.3 KB | Display | PDB format |
PDBx/mmJSON format | 4q68.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/4q68 ftp://data.pdbj.org/pub/pdb/validation_reports/q6/4q68 | HTTPS FTP |
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-Related structure data
Related structure data | 4h4jSC 4q5kC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26898.617 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides uniformis ATCC 8492 (bacteria) Gene: BACUNI_02947 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7V5T8 | ||||
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#2: Sugar | ChemComp-NAG / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT (24-262) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (24-262) WAS EXPRESSED WITH A PURIFICATI | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.44 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 30.00% polyethylene glycol 1500, 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: BL14-1 / Wavelength: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 18, 2014 Details: Vertical focusing mirror; double crystal Si(111) monochromator | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.07→46.47 Å / Num. obs: 93219 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Redundancy: 3.93 % / Biso Wilson estimate: 11.481 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 22.87 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4H4J Resolution: 1.07→39.355 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.976 / Occupancy max: 1 / Occupancy min: 0.07 / SU B: 0.72 / SU ML: 0.016 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.025 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 3. N-ACETYL-GLUCOSAMINE (NAG) MODELED WAS PRESENT IN CRYSTALLIZATION CONDITION. 4. SODIUM IONS WERE PRESENT IN PROTEIN BUFFER AND WERE ASSIGNED TENTATIVELY BASED ON DENSITY AND COORDINATION. 5. CRYTALS WERE OBTAINED BY COCROSTALLIZATION IN PRESENCE OF 1.2 MILLIMOLAR GLCNAC.
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73 Å2 / Biso mean: 12.8506 Å2 / Biso min: 4.04 Å2
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Refinement step | Cycle: LAST / Resolution: 1.07→39.355 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.07→1.098 Å / Total num. of bins used: 20
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