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- PDB-4pqx: Crystal structure of a NigD-like protein (BACCAC_02139) from Bact... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4pqx | ||||||
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Title | Crystal structure of a NigD-like protein (BACCAC_02139) from Bacteroides caccae ATCC 43185 at 2.39 A resolution | ||||||
![]() | Uncharacterized protein | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / NigD-like protein / PF12667 family / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | ![]() NigD-like, C-terminal beta sandwich domain / NigD-like N-terminal OB domain / NigD-like, C-terminal beta sandwich domain / NigD-like, C-terminal domain superfamily / NigD-like N-terminal OB domain / NigD-like C-terminal beta sandwich domain / NigD-like N-terminal OB domain / NigD-like, N-terminal domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Immunoglobulin-like ...NigD-like, C-terminal beta sandwich domain / NigD-like N-terminal OB domain / NigD-like, C-terminal beta sandwich domain / NigD-like, C-terminal domain superfamily / NigD-like N-terminal OB domain / NigD-like C-terminal beta sandwich domain / NigD-like N-terminal OB domain / NigD-like, N-terminal domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Crystal structure of a hypothetical protein (BACCAC_02139) from Bacteroides caccae ATCC 43185 at 2.39 A resolution (CASP Target) Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 360.8 KB | Display | ![]() |
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PDB format | ![]() | 299.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Details | CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. |
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Components
#1: Protein | Mass: 25496.402 Da / Num. of mol.: 4 / Fragment: UNP residues 27-242 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-IPA / #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Sequence details | THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATI | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.66 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 5.00% Glycerol, 21.00% polyethylene glycol 4000, 13.00% 2-propanol, 0.1M sodium citrate - citric acid pH 5.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2013 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.39→48.614 Å / Num. obs: 42698 / % possible obs: 99 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 56.503 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 14.45 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() 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. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 5. EDO, IPA, AND GOL MODELED ARE PRESENT IN CRYSTALLIZATION CONDITIONS.
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Displacement parameters | Biso max: 146.34 Å2 / Biso mean: 54.3673 Å2 / Biso min: 21.88 Å2
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Refine analyze | Luzzati coordinate error obs: 0.306 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.39→48.614 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.39→2.45 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 |
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