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Yorodumi- PDB-3zto: Orthorhombic crystal form C222 of the Aquifex aeolicus nucleoside... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zto | ||||||
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Title | Orthorhombic crystal form C222 of the Aquifex aeolicus nucleoside diphosphate kinase | ||||||
Components | NUCLEOSIDE DIPHOSPHATE KINASE | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information purine nucleotide metabolic process / pyrimidine nucleotide metabolic process / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | AQUIFEX AEOLICUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å | ||||||
Authors | Boissier, F. / Georgescauld, F. / Moynie, L. / Dupuy, J.-W. / Sarger, C. / Podar, M. / Lascu, I. / Giraud, M.-F. / Dautant, A. | ||||||
Citation | Journal: Proteins / Year: 2012 Title: An Intersubunit Disulfide Bridge Stabilizes the Tetrameric Nucleoside Diphosphate Kinase of Aquifex Aeolicus. Authors: Boissier, F. / Georgescauld, F. / Moynie, L. / Dupuy, J. / Sarger, C. / Podar, M. / Lascu, I. / Giraud, M. / Dautant, A. #1: Journal: Proteins / Year: 2007 Title: The Structure of the Escherichia Coli Nucleoside Diphosphate Kinase Reveals a New Quaternary Architecture for This Enzyme Family. Authors: Moynie, L. / Giraud, M. / Georgescauld, F. / Lascu, I. / Dautant, A. #2: Journal: J.Mol.Biol. / Year: 1993 Title: Crystal Structure of Myxococcus Xanthus Nucleoside Diphosphate Kinase and its Interaction with a Nucleotide Substrate at 2.0 A Resolution. Authors: Williams, R.L. / Oren, D.A. / Munoz-Dorado, J. / Inouye, S. / Inouye, M. / Arnold, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zto.cif.gz | 99.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zto.ent.gz | 77.6 KB | Display | PDB format |
PDBx/mmJSON format | 3zto.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zto_validation.pdf.gz | 421.4 KB | Display | wwPDB validaton report |
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Full document | 3zto_full_validation.pdf.gz | 421.4 KB | Display | |
Data in XML | 3zto_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 3zto_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zt/3zto ftp://data.pdbj.org/pub/pdb/validation_reports/zt/3zto | HTTPS FTP |
-Related structure data
Related structure data | 3ztpC 3ztqC 3ztrC 3ztsC 1nlkS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 15963.325 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) AQUIFEX AEOLICUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O67528, nucleoside-diphosphate kinase | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42 % / Description: NONE |
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Crystal grow | pH: 5.5 / Details: 25% PEG 3350, 0.2 M LISO4, 0.1 M BIS-TRIS PH 5.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2008 / Details: KIRKPATRICK BAEZ |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→15.54 Å / Num. obs: 23200 / % possible obs: 99 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Biso Wilson estimate: 13.08 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.47→1.55 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.4 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NLK Resolution: 1.47→15.763 Å / SU ML: 0.15 / σ(F): 0 / Phase error: 16.51 / Stereochemistry target values: ML Details: IN THE SSBOND CARDS: THE FIRST ATOM BELONGS TO THE ALTERNATE CONFORMER A (WITH OCCUPANCY Q1). THE SECOND ONE BELONGS TO THE ALTERNATE CONFORMER B (WITH OCCUPANCY Q2). ABS(Q1 - Q2)*100 IS THE ...Details: IN THE SSBOND CARDS: THE FIRST ATOM BELONGS TO THE ALTERNATE CONFORMER A (WITH OCCUPANCY Q1). THE SECOND ONE BELONGS TO THE ALTERNATE CONFORMER B (WITH OCCUPANCY Q2). ABS(Q1 - Q2)*100 IS THE PERCENTAGE OF CYS133 NOT INVOLVED IN THE DISULFIDE BRIDGE.
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Solvent computation | Shrinkage radii: 0.41 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.145 Å2 / ksol: 0.501 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.3 Å2
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Refinement step | Cycle: LAST / Resolution: 1.47→15.763 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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