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Yorodumi- PDB-1zko: Crystal structure of Glycine cleavage system H protein (tm0212) f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zko | ||||||
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Title | Crystal structure of Glycine cleavage system H protein (tm0212) from Thermotoga maritima at 1.65 A resolution | ||||||
Components | Glycine cleavage system H protein | ||||||
Keywords | Glycine cleavage H-protein / tm0212 / Glycine cleavage system H protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI | ||||||
Function / homology | Function and homology information glycine cleavage complex / glycine decarboxylation via glycine cleavage system / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of Glycine cleavage system H protein (tm0212) from Thermotoga maritima at 1.65 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Remark 999 | SEQUENCE CLONING ARTIFACT: IN THE CLONING CONSTRUCT, THE START CODON WAS CHANGED FROM ATG TO TTG. ...SEQUENCE CLONING ARTIFACT: IN THE CLONING CONSTRUCT, THE START CODON WAS CHANGED FROM ATG TO TTG. AS A RESULT, THE FIRST METHIONINE RESIDUE IS MUTATED TO LEUCINE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zko.cif.gz | 67.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zko.ent.gz | 52.2 KB | Display | PDB format |
PDBx/mmJSON format | 1zko.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/1zko ftp://data.pdbj.org/pub/pdb/validation_reports/zk/1zko | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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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 label comp-ID: HIS / End label comp-ID: GLN / Refine code: 6 / Auth seq-ID: -4 - 123 / Label seq-ID: 8 - 135
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-Components
#1: Protein | Mass: 15513.833 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: gcvH / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WY55 #2: Chemical | ChemComp-NA / | #3: Water | ChemComp-HOH / | |
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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: 1.87 Å3/Da / Density % sol: 33.63 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4 Details: 1.0M LiCl, 30.0% PEG-6000, 0.1M Citrate pH 4.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.946415, 0.979129, 0.979494 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 4, 2005 / Details: Flat mirror (vertical focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: single crystal Si(111) bent monochromator(horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.56→42.53 Å / Num. obs: 30875 / % possible obs: 87.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 6.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.65→42.53 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.538 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.135 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. THE R AND R-FREE FACTORS ARE HIGH DESPITE THE RESOLUTION. ONE REASON MAY BE THAT THE DIFFRACTION IMAGES SHOW DIFFRACTION FROM MORE THAN ONE CRYSTAL. THE ELECTRON DENSITY MAPS ARE VERY ...Details: 1. THE R AND R-FREE FACTORS ARE HIGH DESPITE THE RESOLUTION. ONE REASON MAY BE THAT THE DIFFRACTION IMAGES SHOW DIFFRACTION FROM MORE THAN ONE CRYSTAL. THE ELECTRON DENSITY MAPS ARE VERY CLEAR FOR THE TWO MONOMERS IN THE ASYMMETRIC UNIT.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.464 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→42.53 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 950 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.651→1.693 Å / Total num. of bins used: 20
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