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Yorodumi- PDB-3d4r: CRYSTAL STRUCTURE OF a DUF2118 family protein (MMP0046) FROM METH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d4r | ||||||
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Title | CRYSTAL STRUCTURE OF a DUF2118 family protein (MMP0046) FROM METHANOCOCCUS MARIPALUDIS AT 2.20 A RESOLUTION | ||||||
Components | Domain of Unknown Function from the Pfam-B_34464 Family | ||||||
Keywords | UNKNOWN FUNCTION / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2 | ||||||
Function / homology | Function and homology information Lipocalin - #400 / Protein of unknown function DUF2118 / Uncharacterized protein conserved in archaea (DUF2118) / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Lipocalin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Methanococcus maripaludis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of Domain of Unknown Function from the Pfam-B_34464 Family (NP_987166.1) from Methanococcus maripaludis JJ (DSM 2067) at 2.20 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d4r.cif.gz | 207.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d4r.ent.gz | 169.7 KB | Display | PDB format |
PDBx/mmJSON format | 3d4r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3d4r_validation.pdf.gz | 509.4 KB | Display | wwPDB validaton report |
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Full document | 3d4r_full_validation.pdf.gz | 522.9 KB | Display | |
Data in XML | 3d4r_validation.xml.gz | 41.5 KB | Display | |
Data in CIF | 3d4r_validation.cif.gz | 59.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/3d4r ftp://data.pdbj.org/pub/pdb/validation_reports/d4/3d4r | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Beg label comp-ID: GLY / End label comp-ID: GLU / Refine code: 6 / Auth seq-ID: 10 - 150 / Label seq-ID: 29 - 169
NCS ensembles :
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Details | AUTHORS STATE THAT THE PROTOMER MAY FORM A DIMER BASED ON CRYSTAL PACKING ANALYSIS. ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIC STATE. |
-Components
#1: Protein | Mass: 19813.730 Da / Num. of mol.: 6 / Mutation: F74L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanococcus maripaludis (archaea) / Strain: JJ [DSM 2067] / Gene: NP_987166.1, MMP0046 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q6M171 #2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-PEG / | #4: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE STRAIN CLONED, ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATI | |
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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: 2.79 Å3/Da / Density % sol: 55.89 % |
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Crystal grow | Temperature: 277 K Details: 21.5% polyethylene glycol 3350, 0.214M ammonium citrate, 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: BL9-2 / Wavelength: 0.91837,0.97929,0.97913 | ||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 17, 2008 / Details: FLAT COLLIMATING MIRROR, TOROID FOCUSING MIRROR | ||||||||||||
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.2→28.94 Å / Num. obs: 68137 / % possible obs: 100 % | ||||||||||||
Reflection shell | Resolution: 2.2→2.26 Å / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 1.1 / % possible all: 100 |
-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.2→28.94 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / SU B: 10.816 / SU ML: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. EDO WAS MODELED BASED ON CRYO CONDITIONS. 4. RAMACHANDRAN OUTLIERS A50 AND C50 ARE IN GOOD DENSITY.
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Solvent computation | Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.66 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→28.94 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.2→2.26 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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