+Open data
-Basic information
Entry | Database: PDB / ID: 3cax | ||||||
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Title | Crystal structure of uncharacterized protein PF0695 | ||||||
Components | Uncharacterized protein PF0695 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information Domain of unknown function DUF438 / Family of unknown function (DUF438) / PAS domain / nmb1532 protein domain like / Hemerythrin-like / Hemerythrin HHE cation binding domain / PAS domain / Beta-Lactamase / Four Helix Bundle (Hemerythrin (Met), subunit A) / PAS domain superfamily ...Domain of unknown function DUF438 / Family of unknown function (DUF438) / PAS domain / nmb1532 protein domain like / Hemerythrin-like / Hemerythrin HHE cation binding domain / PAS domain / Beta-Lactamase / Four Helix Bundle (Hemerythrin (Met), subunit A) / PAS domain superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Pyrococcus furiosus DSM 3638 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.43 Å | ||||||
Authors | Ramagopal, U.A. / Hu, S. / Toro, R. / Gilmore, M. / Bain, K. / Meyer, A.J. / Rodgers, L. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of uncharacterized protein PF0695. Authors: Ramagopal, U.A. / Hu, S. / Toro, R. / Gilmore, M. / Bain, K. / Meyer, A.J. / Rodgers, L. / Sauder, J.M. / Burley, S.K. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cax.cif.gz | 87.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cax.ent.gz | 66.6 KB | Display | PDB format |
PDBx/mmJSON format | 3cax.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ca/3cax ftp://data.pdbj.org/pub/pdb/validation_reports/ca/3cax | HTTPS FTP |
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-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: 43614.312 Da / Num. of mol.: 1 / Fragment: Residues 118-475 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Species: Pyrococcus furiosus / Strain: DSM 3638 / JCM 8422 / Vc1 / Gene: PF0695 / Plasmid: BC-pSGX4(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8U2Y3 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.73 Å3/Da / Density % sol: 67.02 % Description: The data set that was collected at the NSLS beamline X4C has been used for SAD |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2M Ammonium(tri-)citrate pH 7.0, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-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: 2.43→50 Å / Num. all: 24050 / Num. obs: 24050 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12 % / Rmerge(I) obs: 0.107 / Χ2: 1.116 / Net I/σ(I): 7.7 | |||||||||||||||
Reflection shell | Resolution: 2.43→2.49 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.744 / Mean I/σ(I) obs: 2.74 / Num. unique all: 2337 / Rsym value: 0.547 / Χ2: 0.567 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.43→34.69 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 13.852 / SU ML: 0.155 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.248 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.504 Å2
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Refinement step | Cycle: LAST / Resolution: 2.43→34.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.43→2.494 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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