- PDB-4q5k: Crystal structure of a N-acetylmuramoyl-L-alanine amidase (BACUNI... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4q5k
Title
Crystal structure of a N-acetylmuramoyl-L-alanine amidase (BACUNI_02947) from Bacteroides uniformis ATCC 8492 at 1.30 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
Mass: 18.015 Da / Num. of mol.: 455 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE CONSTRUCT (24-262) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (24-262) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 29% polyethylene glycol 4000, 0.1mM Tris pH8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution: 1.3→40.061 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.974 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 1.382 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.041 / 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-1,6-ANHYDRO-N-ACETYLMURAMIC ACID (GML) MODELED WAS PRESENT IN CRYSTALLIZATION CONDITION. 4. DENSITIES FOR THE LOOP 79-83 ARE WEAK. 5. CRYTALS WERE OBTAINED BY COCROSTALLIZATION IN PRESENCE OF 0.93 MILLIMOLAR GLCNAC-1,6-ANHYDRO-MURNAC.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1494
2940
4.9 %
RANDOM
Rwork
0.1156
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obs
0.1173
60203
99.87 %
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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
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