+Open data
-Basic information
Entry | Database: PDB / ID: 3d5l | ||||||
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Title | Crystal structure of regulatory protein RecX | ||||||
Components | Regulatory protein RecX | ||||||
Keywords | SIGNALING PROTEIN / PSI-II / NYSGXRC / RecX / DNA repair / 10123k / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Lactobacillus reuteri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å | ||||||
Authors | Agarwal, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of DNA repair regulatory protein RecX. Authors: Agarwal, R. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d5l.cif.gz | 91.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d5l.ent.gz | 70.9 KB | Display | PDB format |
PDBx/mmJSON format | 3d5l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3d5l_validation.pdf.gz | 447.5 KB | Display | wwPDB validaton report |
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Full document | 3d5l_full_validation.pdf.gz | 454.8 KB | Display | |
Data in XML | 3d5l_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 3d5l_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/3d5l ftp://data.pdbj.org/pub/pdb/validation_reports/d5/3d5l | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25598.324 Da / Num. of mol.: 2 / Fragment: Residues 2-211 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus reuteri (bacteria) / Strain: 100-23 / Gene: Lreu23DRAFT_0930 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)(RIPL) / References: UniProt: Q1U8Q6, UniProt: B3XNW8*PLUS #2: Chemical | ChemComp-SO4 / | #3: 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: 2.71 Å3/Da / Density % sol: 54.68 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 200mM Ammonium sulfate, 25% PEG 3350, 100mM Bis-tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 22, 2008 / Details: Mirrors |
Radiation | Monochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→50 Å / Num. all: 23443 / Num. obs: 23443 / % possible obs: 92.4 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.27→2.35 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 1 / Num. unique all: 1363 / % possible all: 55.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.35→41.59 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 62466.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 21.1398 Å2 / ksol: 0.344102 e/Å3 | |||||||||||||||||||||
Displacement parameters | Biso mean: 27.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.35→41.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.5 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
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Xplor file |
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