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Yorodumi- PDB-2p97: CRYSTAL STRUCTURE OF A PUTATIVE METAL-DEPENDENT HYDROLASE (AVA_30... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2p97 | ||||||
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Title | CRYSTAL STRUCTURE OF A PUTATIVE METAL-DEPENDENT HYDROLASE (AVA_3068) FROM ANABAENA VARIABILIS ATCC 29413 AT 1.65 A RESOLUTION | ||||||
Components | Hypothetical protein | ||||||
Keywords | METAL BINDING PROTEIN / PUTATIVE METAL-DEPENDENT HYDROLASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2 | ||||||
Function / homology | Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / metal ion binding / Alpha Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Anabaena variabilis ATCC 29413 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of hypothetical protein (YP_323572.1) from Anabaena variabilis ATCC 29413 at 1.65 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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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 | 2p97.cif.gz | 107.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p97.ent.gz | 85.5 KB | Display | PDB format |
PDBx/mmJSON format | 2p97.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/2p97 ftp://data.pdbj.org/pub/pdb/validation_reports/p9/2p97 | 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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3 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
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-Components
#1: Protein | Mass: 22546.295 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anabaena variabilis ATCC 29413 (bacteria) Species: Anabaena variabilis / Strain: PCC 7937 / Gene: YP_323572.1, Ava_3068 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q3M8K9 #2: Chemical | #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal |
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Crystal grow |
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.65→29.488 Å / Num. obs: 63319 / % possible obs: 96.4 % / Biso Wilson estimate: 29.985 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 14.57 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1,2
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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: 1.65→29.488 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.225 / SU ML: 0.056 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.081 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. 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. 4. TWO MAGNESIUM IONS FROM CRYSTALLIZATION ARE MODELED IN SUBUNIT. 5. ONE CHLORIDE ION FROM CRYSTALLIZATION WAS MODELED. 6. THERE IS A DUAL CONFORMATION IN SUBUNIT A FROM RESIDUE 16 TO 23.
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.44 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→29.488 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.65→1.693 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 | Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 0 - 200 / Label seq-ID: 1 - 201
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