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Yorodumi- PDB-2qjw: CRYSTAL STRUCTURE OF A PUTATIVE HYDROLASE OF THE ALPHA/BETA SUPER... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qjw | ||||||
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Title | CRYSTAL STRUCTURE OF A PUTATIVE HYDROLASE OF THE ALPHA/BETA SUPERFAMILY (XCC1541) FROM XANTHOMONAS CAMPESTRIS PV. CAMPESTRIS AT 1.35 A RESOLUTION | ||||||
Components | Uncharacterized protein XCC1541 | ||||||
Keywords | HYDROLASE / PUTATIVE HYDROLASE OF THE ALPHA/BETA SUPERFAMILY / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2 | ||||||
Function / homology | Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / DI(HYDROXYETHYL)ETHER / L(+)-TARTARIC ACID / Uncharacterized protein Function and homology information | ||||||
Biological species | Xanthomonas campestris pv. campestris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.35 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of uncharacterized protein XCC1541 (NP_636912.1) from Xanthomonas campestris at 1.35 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Remark 300 | BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF FOUR ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF FOUR CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE. | ||||||
Remark 999 | SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qjw.cif.gz | 162 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qjw.ent.gz | 130.4 KB | Display | PDB format |
PDBx/mmJSON format | 2qjw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/2qjw ftp://data.pdbj.org/pub/pdb/validation_reports/qj/2qjw | 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ARG / End label comp-ID: LEU / Refine code: 5 / Auth seq-ID: 3 - 175 / Label seq-ID: 4 - 176
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Details | SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE. |
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 18935.289 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria) Species: Xanthomonas campestris / Strain: NCPPB 528, LMG 568 / Gene: NP_636912.1, XCC1541 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8PAE4 |
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-Non-polymers , 5 types, 781 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-TLA / | #4: Chemical | ChemComp-PEG / #5: Chemical | ChemComp-P6G / | #6: Water | ChemComp-HOH / | |
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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: 2.14 Å3/Da / Density % sol: 42.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: NANODROP, 0.264M Di-ammonium tartrate, 15.8% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97920 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 3, 2007 / Details: Flat mirror (vertical focusing) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal Si(111) bent (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.35→29.775 Å / Num. obs: 140150 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.984 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 10.76 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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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: 1.35→29.775 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.211 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.064 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. CHLORIDE IONS, TARTRATE ION AND THE FRAGMENTS OF POLYETHYLENE GLYCOL 400 MOLECULE WITH DIFFERENT MOLECULAR WEIGHT WERE MODELED IN THIS STRUCTURE. 4. RESIDUES 71 TO 75 IN SUBUNIT D ARE DISORDERED AND NOT MODELED IN THE STRUCTURE. 5. UNEXPLAINED ELECTRON DENSITY NEAR RESIDUES A147 AND D147 ARE NOT MODELED. THEY ARE SUGGESTED AS NITROBENZENE (NBZ).
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.979 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→29.775 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.35→1.384 Å / Total num. of bins used: 20
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