[English] 日本語
Yorodumi- PDB-2ew0: X-ray Crystal Structure of Protein Q6FF54 from Acinetobacter sp. ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ew0 | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray Crystal Structure of Protein Q6FF54 from Acinetobacter sp. ADP1. Northeast Structural Genomics Consortium Target AsR1. | ||||||
Components | hypothetical protein ACIAD0353 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Q5FF54 / AsR1 / NESG / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | VC0467-like / VC0467-like / Protein of unknown function UPF0301 / Uncharacterized ACR, COG1678 / 3-Layer(aba) Sandwich / Alpha Beta / UPF0301 protein ACIAD0353 Function and homology information | ||||||
Biological species | Acinetobacter sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å | ||||||
Authors | Kuzin, A.P. / Abashidze, M. / Vorobiev, S.M. / Forouhar, F. / Acton, T. / Xiao, R. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: TO BE PUBLISHED Title: Novel x-ray structure of hypothetical protein Q6FF54 at the resolution 1.4 A. Northeast Structural Genomics target AsR1. Authors: Kuzin, A.P. / Abashidze, M. / Vorobiev, S.M. / Forouhar, F. / Acton, T. / Xiao, R. / Ma, L.-C. / Cunningham, K.E. / Montelione, G.T. / Hunt, J.F. | ||||||
History |
| ||||||
Remark 999 | sequence DNA sequencing of the expression clone for this protein indicated 17 amino acid ...sequence DNA sequencing of the expression clone for this protein indicated 17 amino acid substitutions among the 184 residues in protein Q6FF54 as inferred from the genome sequence of Acinetobacter sp.. The electron density at each of these sites was consistent with the sequence of the expression plasmid and in most cases clearly inconsistent with the reported genome sequence. Authors assume that these differences arise from sequence variations among Acinetobacter strains but have not pursued additional experimental investigations of their origin. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ew0.cif.gz | 49.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ew0.ent.gz | 38.1 KB | Display | PDB format |
PDBx/mmJSON format | 2ew0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ew0_validation.pdf.gz | 441.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2ew0_full_validation.pdf.gz | 443.6 KB | Display | |
Data in XML | 2ew0_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 2ew0_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ew/2ew0 ftp://data.pdbj.org/pub/pdb/validation_reports/ew/2ew0 | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 21667.900 Da / Num. of mol.: 1 Mutation: D34E, L40I, S46A, V50I, R51K, E60D, H63N, Q65N, V89T, L100V, T131G, G137D, S140A, E161D, L170I, I175T, S178A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter sp. (bacteria) / Strain: ADP1 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) + Magic / References: UniProt: Q6FF54 | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.95 % Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS. |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2M (NH4)2SO4, 2% PEG400, 0.1M MES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 15, 2005 / Details: mirrors |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. obs: 85882 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 24.4 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 72.8 |
Reflection shell | Resolution: 1.4→1.45 Å / Rmerge(I) obs: 0.374 / % possible all: 99.6 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.4→29.22 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 395945.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: THE FRIEDEL PAIRS WERE USED FOR phasing.
| ||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.1504 Å2 / ksol: 0.402761 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 19.4 Å2
| ||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→29.22 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
LS refinement shell | Resolution: 1.4→1.49 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
| ||||||||||||||||||||
Xplor file |
|