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Yorodumi- PDB-2j5t: Glutamate 5-kinase from Escherichia coli complexed with glutamate -
+Open data
-Basic information
Entry | Database: PDB / ID: 2j5t | ||||||
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Title | Glutamate 5-kinase from Escherichia coli complexed with glutamate | ||||||
Components | GLUTAMATE 5-KINASE | ||||||
Keywords | TRANSFERASE / PROLINE BIOSYNTHESIS / FEEDBACK REGULATION | ||||||
Function / homology | Function and homology information proline binding / glutamate 5-kinase / glutamate 5-kinase activity / L-proline biosynthetic process / proline biosynthetic process / magnesium ion binding / protein homodimerization activity / RNA binding / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Marco-Marin, C. / Gil-Ortiz, F. / Perez-Arellano, I. / Cervera, J. / Fita, I. / Rubio, V. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: A Novel Two-Domain Architecture within the Amino Acid Kinase Enzyme Family Revealed by the Crystal Structure of Escherichia Coli Glutamate 5-Kinase. Authors: Marco-Marin, C. / Gil-Ortiz, F. / Perez-Arellano, I. / Cervera, J. / Fita, I. / Rubio, V. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2j5t.cif.gz | 518.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j5t.ent.gz | 427.8 KB | Display | PDB format |
PDBx/mmJSON format | 2j5t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2j5t_validation.pdf.gz | 540.3 KB | Display | wwPDB validaton report |
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Full document | 2j5t_full_validation.pdf.gz | 579.8 KB | Display | |
Data in XML | 2j5t_validation.xml.gz | 93.7 KB | Display | |
Data in CIF | 2j5t_validation.cif.gz | 123.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j5/2j5t ftp://data.pdbj.org/pub/pdb/validation_reports/j5/2j5t | HTTPS FTP |
-Related structure data
Related structure data | 2j5vSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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5 |
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6 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 4 / Auth seq-ID: 3 - 367 / Label seq-ID: 3 - 367
NCS oper:
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Details | CONTACTS BETWEEN DIMERS ARE WEAK, BUT GEL FILTRATION EXPERIMENTS SHOW THAT THE PROTEIN IS TETRAMERIC AND THE TETRAMERS FORMED IN THE CRYSTAL ARE EQUIVALENT TO THOSE FOUNDIN A DIFFERENT CRYSTAL OF THIS PROTEIN (WITH DIFFERENT SPACEGROUP). |
-Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 39089.430 Da / Num. of mol.: 8 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A7B5, glutamate 5-kinase |
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-Non-polymers , 5 types, 151 molecules
#2: Chemical | ChemComp-GLU / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-MG / #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, ILE 129 TO VAL ENGINEERED RESIDUE IN CHAIN B, ILE 129 TO VAL ...ENGINEERED |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.2 % |
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Crystal grow | pH: 6.5 / Details: 1.45 M MGSO4, 20 MM CACL2, 0.1 M MES PH 6.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 6, 2005 / Details: TOROIDAL MIRRORS |
Radiation | Monochromator: SI(111) AND SI (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 74908 / % possible obs: 99.3 % / Observed criterion σ(I): 2.9 / Redundancy: 4.5 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.9 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PARTIALLY-REFINED MODEL OF PBD ENTRY 2J5V Resolution: 2.9→25 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.874 / SU B: 35.798 / SU ML: 0.302 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.401 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FINAL STRUCTURE ENCOMPASSES THE ENTIRE POLYPEPTIDE CHAIN FROM RESIDUE 3 IN SUBUNITS D AND E, BUT LACKS THE FOLLOWING RESIDUES IN THE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FINAL STRUCTURE ENCOMPASSES THE ENTIRE POLYPEPTIDE CHAIN FROM RESIDUE 3 IN SUBUNITS D AND E, BUT LACKS THE FOLLOWING RESIDUES IN THE OTHER SUBUNITS, 202-211 (A), 202-213 AND 367 (B), 203-211 (G AND C), 176-185 AND 196- 213 (H), 203-213 (F).
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.57 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→25 Å
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Refine LS restraints |
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