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Yorodumi- PDB-2hkv: CRYSTAL STRUCTURE OF A PUTATIVE MEMBER OF THE DINB FAMILY (EXIG_1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hkv | ||||||
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Title | CRYSTAL STRUCTURE OF A PUTATIVE MEMBER OF THE DINB FAMILY (EXIG_1237) FROM EXIGUOBACTERIUM SIBIRICUM 255-15 AT 1.70 A RESOLUTION | ||||||
Components | Hypothetical protein | ||||||
Keywords | DNA BINDING PROTEIN / PUTATIVE MEMBER OF THE DINB FAMILY / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2 | ||||||
Function / homology | Function and homology information DNA damage-inducible protein DinB / DinB family / dinb family like domain / DinB/YfiT-like putative metalloenzymes / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | Exiguobacterium sibiricum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of conserved hypothetical protein RBL00553 (ZP_00537729.1) from EXIGUOBACTERIUM SP. 255-15 at 1.70 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 | 2hkv.cif.gz | 43.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hkv.ent.gz | 32.4 KB | Display | PDB format |
PDBx/mmJSON format | 2hkv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hkv_validation.pdf.gz | 425 KB | Display | wwPDB validaton report |
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Full document | 2hkv_full_validation.pdf.gz | 427.5 KB | Display | |
Data in XML | 2hkv_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 2hkv_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hk/2hkv ftp://data.pdbj.org/pub/pdb/validation_reports/hk/2hkv | HTTPS FTP |
-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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Unit cell |
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-Components
#1: Protein | Mass: 17371.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Exiguobacterium sibiricum (bacteria) / Strain: 255-15 / Gene: ZP_00537729.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q41IB9, UniProt: B1YEV7*PLUS | ||
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#2: Chemical | ChemComp-NI / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: 1.7→25.094 Å / Num. obs: 17704 / % possible obs: 99.8 % / Redundancy: 9.38 % / Biso Wilson estimate: 37.034 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 9.58 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.7→25.094 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 6.318 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.111 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 0.7 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. THE ASSIGNMENT OF THE METAL AS PREDOMINATELY NICKEL IS BASED ON BOTH X-RAY FLUORECENCE METAL SCAN AND DIFFERENCE MAPS (ABOVE AND BELOW NICKEL AND ZINC EDGES). 5. THE ASSIGNMENT OF CHLORIDES ARE BASED ON DIFFERENCE DENSITY. 6. THE DISORDER ON TWO-FOLD BY RESIDUE 4 INDICATED THAT THE SPACE GROUP IS NOT STRICTLY P3221 BUT P32, REFINEMENT IN P3221 RESULTS ONLY ~1% INCREASE IN RFACTOR AND RFREE COMPARED TO P32, THUS THE SPACE GROUP WAS ASSIGNED AS HIGHER SYMMETRY P3221. 7. THE EXPERIMENTAL PHASES ARE FROM A DIFFERENT CRYSTAL, THEY ARE USED AS RESTRAINTS IN REFINEMENT. 8. DENSITY FOR RESIDUE 99 IS POOR.
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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: 33.948 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→25.094 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 7.135 Å / Origin y: -0.881 Å / Origin z: -8.439 Å
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Refinement TLS group | Selection: ALL |