[English] 日本語
Yorodumi- PDB-3hix: Crystal Structure of the Rhodanese_3 like domain from Anabaena sp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hix | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the Rhodanese_3 like domain from Anabaena sp Alr3790 protein. Northeast Structural Genomics Consortium Target NsR437i | ||||||
Components | Alr3790 protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Alr3790 / rhodanese / rhodanese_3 / Q8YQN0 / Q8YQN0_ANASP / NSR437I / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | Function and homology information Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Anabaena sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.92 Å | ||||||
Authors | 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) | ||||||
Citation | Journal: To be Published 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3hix.cif.gz | 118.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3hix.ent.gz | 98.6 KB | Display | PDB format |
PDBx/mmJSON format | 3hix.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/3hix ftp://data.pdbj.org/pub/pdb/validation_reports/hi/3hix | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
5 |
| ||||||||
Unit cell |
|
-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.) Anabaena sp. (bacteria) / Strain: PCC 7120 / Gene: alr3790 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q8YQN0 #2: Chemical | ChemComp-MN / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.47 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9786 |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.92→34.61 Å / SU ML: 0.43 / σ(F): 1.91 / Stereochemistry target values: ML 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.92→34.61 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|