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Yorodumi- PDB-3gir: Crystal structure of glycine cleavage system aminomethyltransfera... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gir | ||||||
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Title | Crystal structure of glycine cleavage system aminomethyltransferase T from Bartonella henselae | ||||||
Components | Aminomethyltransferase | ||||||
Keywords | TRANSFERASE / BARTONELLA HENSELAE / GLYCINE CLEAVAGE SYSTEM / AMINOMETHYLTRANSFERASE / Aminotransferase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID | ||||||
Function / homology | Function and homology information aminomethyltransferase / glycine catabolic process / aminomethyltransferase activity / transaminase activity Similarity search - Function | ||||||
Biological species | Bartonella henselae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molecular replacement, molecular replacement / Resolution: 1.6 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: To be Published Title: Crystal structure of glycine cleavage system aminomethyltransferase T from Bartonella henselae Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gir.cif.gz | 98.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gir.ent.gz | 72.5 KB | Display | PDB format |
PDBx/mmJSON format | 3gir.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gir_validation.pdf.gz | 424.5 KB | Display | wwPDB validaton report |
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Full document | 3gir_full_validation.pdf.gz | 425.4 KB | Display | |
Data in XML | 3gir_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 3gir_validation.cif.gz | 32.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/3gir ftp://data.pdbj.org/pub/pdb/validation_reports/gi/3gir | HTTPS FTP |
-Related structure data
Related structure data | 1wsrS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42890.066 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bartonella henselae (bacteria) / Strain: HUSTON-1 / Gene: gcvT, BH12840 / Plasmid: AVA0421 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q6G2E9, UniProt: A0A0H3M6H9*PLUS, aminomethyltransferase |
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#2: Chemical | ChemComp-NA / |
#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: 3.21 Å3/Da / Density % sol: 61.73 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop Details: PROPLEX SCREEN, H4: 1.4M NA MALONATE, BAHEA.00657.A AT 44.8 MG/ML, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9765 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→69.01 Å / Num. all: 70368 / Num. obs: 70368 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 26.43 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 16.45 |
Reflection shell | Resolution: 1.6→1.64 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 2.6 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement, molecular replacement Starting model: pdb entry 1wsr, modified with ccp4 program chainsaw Resolution: 1.6→69.01 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.401 / SU ML: 0.049 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.91 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→69.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.64 Å / Total num. of bins used: 20
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