+Open data
-Basic information
Entry | Database: PDB / ID: 1wmm | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of PH1033 from Pyrococcus horikoshii Ot3 | ||||||
Components | Hypothetical UPF0310 protein PH1033 | ||||||
Keywords | UNKNOWN FUNCTION / Pyrococcus horikoshii / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Uncharacterised protein family UPF0310 / EVE domain / EVE domain / ph1033 like fold / ph1033 like domains / PUA-like superfamily / Roll / Alpha Beta / UPF0310 protein PH1033 Function and homology information | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å | ||||||
Authors | Sugahara, M. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: Nucleant-mediated protein crystallization with the application of microporous synthetic zeolites. Authors: Sugahara, M. / Asada, Y. / Morikawa, Y. / Kageyama, Y. / Kunishima, N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1wmm.cif.gz | 42.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1wmm.ent.gz | 29.9 KB | Display | PDB format |
PDBx/mmJSON format | 1wmm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wmm_validation.pdf.gz | 419.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1wmm_full_validation.pdf.gz | 422.1 KB | Display | |
Data in XML | 1wmm_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 1wmm_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/1wmm ftp://data.pdbj.org/pub/pdb/validation_reports/wm/1wmm | HTTPS FTP |
-Related structure data
Related structure data | 2dpnC 2hd9C 2zbnC C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a monomer in the asymmetric unit. |
-Components
#1: Protein | Mass: 17464.623 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: O58764 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 60.9 % |
---|---|
Crystal grow | Temperature: 295 K / Method: microbatch / pH: 5.7 / Details: PEG4K, pH 5.7, microbatch, temperature 295K |
-Data collection
Diffraction |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| |||||||||||||||
Detector |
| |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
| |||||||||||||||
Reflection | Resolution: 2.2→40 Å / Num. all: 12147 / Num. obs: 12147 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 45.02 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.055 / Net I/σ(I): 12.3 | |||||||||||||||
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 4.3 / Num. unique all: 1172 / Rsym value: 0.361 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.2→32.48 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.8 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→32.48 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.28 Å / Rfactor Rfree error: 0.05
|