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- PDB-3hix: Crystal Structure of the Rhodanese_3 like domain from Anabaena sp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3hix | ||||||
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Title | Crystal Structure of the Rhodanese_3 like domain from Anabaena sp Alr3790 protein. Northeast Structural Genomics Consortium Target NsR437i | ||||||
![]() | Alr3790 protein | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Alr3790 / rhodanese / rhodanese_3 / Q8YQN0 / Q8YQN0_ANASP / NSR437I / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vorobiev, S. / Chen, Y. / Forouhar, F. / Maglaqui, M. / Ciccosanti, C. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. ...Vorobiev, S. / Chen, Y. / Forouhar, F. / Maglaqui, M. / Ciccosanti, C. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: Crystal Structure of the Rhodanese_3 like domain from Anabaena sp Alr3790 protein. Authors: Vorobiev, S. / Chen, Y. / Forouhar, F. / Maglaqui, M. / Ciccosanti, C. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 118.7 KB | Display | ![]() |
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PDB format | ![]() | 98.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.8 KB | Display | ![]() |
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Full document | ![]() | 452.3 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 20.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 11956.730 Da / Num. of mol.: 3 / Fragment: sequence database residues 24-120 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-MN / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.47 % |
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Crystal grow | Temperature: 277 K / pH: 6 Details: 20% PEG 4000, 0.1M manganese chloride, 0.1M MES, pH 6.0, Microbatch under paraffin oil, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 15, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→500 Å / Num. obs: 21563 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 14.2 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 37.6 |
Reflection shell | Highest resolution: 1.92 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 3.9 / % possible all: 95.5 |
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Processing
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Refinement | Method to determine structure: ![]() Details: TLS DETAILS. NUMBER OF TLS GROUPS: 3 ORIGIN: CENTER OF MASS TLS GROUP : 1 SELECTION: chain A ORIGIN FOR THE GROUP (A): 21.6286 35.3809 -3.2102 T TENSOR T11: 0.0624 T22: 0.1527 T33: 0.1155 ...Details: TLS DETAILS. NUMBER OF TLS GROUPS: 3 ORIGIN: CENTER OF MASS TLS GROUP : 1 SELECTION: chain A ORIGIN FOR THE GROUP (A): 21.6286 35.3809 -3.2102 T TENSOR T11: 0.0624 T22: 0.1527 T33: 0.1155 T12: 0.0177 T13: 0.0028 T23: 0.0021 L TENSOR L11: 1.3258 L22: 0.9000 L33: 1.2612 L12: -0.1670 L13: 1.0507 L23: -0.3704 S TENSOR S11: -0.1360 S12: 0.0069 S13: 0.0464 S21: 0.0477 S22: 0.0383 S23: 0.0000 S31: -0.2015 S32: -0.0132 S33: -0.2878 TLS GROUP : 2 SELECTION: chain B ORIGIN FOR THE GROUP (A): 42.5423 32.7700 24.7352 T TENSOR T11: 0.3628 T22: 0.1203 T33: 0.1251 T12: -0.0085 T13: -0.0376 T23: 0.0201 L TENSOR L11: 1.4097 L22: 0.3349 L33: 0.8316 L12: 0.6542 L13: -0.3603 L23: -0.3371 S TENSOR S11: 0.1203 S12: 0.0108 S13: 0.0659 S21: 0.3051 S22: -0.1410 S23: 0.0289 S31: -0.5626 S32: -0.0803 S33: -0.1710 TLS GROUP : 3 SELECTION: chain C ORIGIN FOR THE GROUP (A): 50.2033 53.9437 13.5016 T TENSOR T11: 0.1434 T22: 0.1161 T33: 0.1814 T12: 0.0063 T13: -0.0092 T23: -0.0202 L TENSOR L11: 0.6296 L22: 0.8678 L33: 0.3256 L12: -0.1594 L13: 0.2343 L23: -0.2656 S TENSOR S11: -0.0424 S12: 0.1661 S13: -0.0522 S21: -0.2500 S22: 0.0465 S23: -0.0200 S31: 0.1290 S32: 0.0377 S33: -0.0000
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.73 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.92→34.61 Å
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Refine LS restraints |
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LS refinement shell |
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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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