+Open data
-Basic information
Entry | Database: PDB / ID: 3hhl | ||||||
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Title | Crystal structure of methylated RPA0582 protein | ||||||
Components | (RPA0582) x 4 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / ALPHA-BETA-BARREL / PSI-2 / PROTEIN STRUCTURE INITIATIVE / REDUCTIVE METHYLATION / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information Domain of unknown function DUF1330 / Domain of unknown function (DUF1330) / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Sledz, P. / Niedzialkowska, E. / Chruszcz, M. / Porebski, P. / Yim, V. / Kudritska, M. / Zimmerman, M.D. / Evdokimova, E. / Savchenko, A. / Edwards, A. ...Sledz, P. / Niedzialkowska, E. / Chruszcz, M. / Porebski, P. / Yim, V. / Kudritska, M. / Zimmerman, M.D. / Evdokimova, E. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of methylated RPA0582 protein Authors: Sledz, P. / Niedzialkowska, E. / Chruszcz, M. / Porebski, P. / Yim, V. / Kudritska, M. / Zimmerman, M.D. / Evdokimova, E. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hhl.cif.gz | 141.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hhl.ent.gz | 110.8 KB | Display | PDB format |
PDBx/mmJSON format | 3hhl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hhl_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3hhl_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3hhl_validation.xml.gz | 28.9 KB | Display | |
Data in CIF | 3hhl_validation.cif.gz | 38.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hh/3hhl ftp://data.pdbj.org/pub/pdb/validation_reports/hh/3hhl | HTTPS FTP |
-Related structure data
Related structure data | 3dcaS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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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: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: MLY / End label comp-ID: MLY / Refine code: 6 / Auth seq-ID: 1 - 135 / Label seq-ID: 2 - 136
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-Components
-Protein , 4 types, 4 molecules ABCD
#1: Protein | Mass: 16333.947 Da / Num. of mol.: 1 / Mutation: F61S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Strain: CGA009 / Gene: RPA0582 / Plasmid: P15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RP / References: UniProt: Q6NC90 |
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#2: Protein | Mass: 16306.900 Da / Num. of mol.: 1 / Mutation: F61S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Strain: CGA009 / Gene: RPA0582 / Plasmid: P15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RP / References: UniProt: Q6NC90 |
#3: Protein | Mass: 16346.965 Da / Num. of mol.: 1 / Mutation: F61S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Strain: CGA009 / Gene: RPA0582 / Plasmid: P15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RP / References: UniProt: Q6NC90 |
#4: Protein | Mass: 16320.928 Da / Num. of mol.: 1 / Mutation: F61S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Strain: CGA009 / Gene: RPA0582 / Plasmid: P15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RP / References: UniProt: Q6NC90 |
-Non-polymers , 10 types, 279 molecules
#5: Chemical | #6: Chemical | ChemComp-CL / #7: Chemical | ChemComp-PEG / #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-GOL / #11: Chemical | #12: Chemical | ChemComp-1PE / | #13: Chemical | #14: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE MUTATION F61S IS A CLONING ARTIFACT THAT WAS CONFIRMED BY SEQUENCING |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M AMMONIUM SULPHATE, 25% PEG3350, 0.1M HEPES pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9787 / Wavelength: 0.9787 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Oct 31, 2007 / Details: MIRROR |
Radiation | Monochromator: SI-111 CHANNEL / Protocol: MOLECULAR REPLACEMENT / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→96.67 Å / Num. all: 47581 / Num. obs: 47581 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 73.8 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 24.26 |
Reflection shell | Resolution: 2.65→2.7 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2405 / Rsym value: 0.596 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3DCA Resolution: 2.65→32.17 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 12.676 / SU ML: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.213 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
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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: 34.56 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→32.17 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Number: 1745 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.65→2.72 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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