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Yorodumi- PDB-2gar: A PH-DEPENDENT STABLIZATION OF AN ACTIVE SITE LOOP OBSERVED FROM ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gar | ||||||
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Title | A PH-DEPENDENT STABLIZATION OF AN ACTIVE SITE LOOP OBSERVED FROM LOW AND HIGH PH CRYSTAL STRUCTURES OF MUTANT MONOMERIC GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE | ||||||
Components | GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE | ||||||
Keywords | PURINE BIOSYNTHESIS / FOLATE COFACTORS / LOOP FLEXIBILITY / MONOMER-DIMER ASSOCIATION / ENZYME MECHANISM / ANTI-CANCER AGENTS | ||||||
Function / homology | Function and homology information phosphoribosylglycinamide formyltransferase 1 / phosphoribosylglycinamide formyltransferase activity / 'de novo' IMP biosynthetic process / DNA damage response / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Su, Y. / Yamashita, M.M. / Greasley, S.E. / Mullen, C.A. / Shim, J.H. / Jennings, P.A. / Benkovic, S.J. / Wilson, I.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: A pH-dependent stabilization of an active site loop observed from low and high pH crystal structures of mutant monomeric glycinamide ribonucleotide transformylase at 1.8 to 1.9 A. Authors: Su, Y. / Yamashita, M.M. / Greasley, S.E. / Mullen, C.A. / Shim, J.H. / Jennings, P.A. / Benkovic, S.J. / Wilson, I.A. #1: Journal: J.Mol.Biol. / Year: 1995 Title: Towards Structure-Based Drug Design: Crystal Structure of a Multisubstrate Adduct Complex of Glycinamide Ribonucleotide Transformylase at 1.96 A Resolution Authors: Klein, C. / Chen, P. / Arevalo, J.H. / Stura, E.A. / Marolewski, A. / Warren, M.S. / Benkovic, S.J. / Wilson, I.A. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992 Title: Structures of Apo and Complexed Escherichia Coli Glycinamide Ribonucleotide Transformylase Authors: Almassy, R.J. / Janson, C.A. / Kan, C.C. / Hostomska, Z. #3: Journal: J.Mol.Biol. / Year: 1992 Title: Crystal Structure of Glycinamide Ribonucleotide Transformylase from Escherichia Coli at 3.0 A Resolution. A Target Enzyme for Chemotherapy Authors: Chen, P. / Schulze-Gahmen, U. / Stura, E.A. / Inglese, J. / Johnson, D.L. / Marolewski, A. / Benkovic, S.J. / Wilson, I.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gar.cif.gz | 51.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gar.ent.gz | 36.1 KB | Display | PDB format |
PDBx/mmJSON format | 2gar.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gar_validation.pdf.gz | 383.3 KB | Display | wwPDB validaton report |
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Full document | 2gar_full_validation.pdf.gz | 385.3 KB | Display | |
Data in XML | 2gar_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | 2gar_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ga/2gar ftp://data.pdbj.org/pub/pdb/validation_reports/ga/2gar | HTTPS FTP |
-Related structure data
Related structure data | 3garC 1garS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23208.217 Da / Num. of mol.: 1 / Mutation: E70A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) References: UniProt: P08179, phosphoribosylglycinamide formyltransferase 1 |
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#2: Chemical | ChemComp-PO4 / |
#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: 2.2 Å3/Da / Density % sol: 44 % | |||||||||||||||
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Crystal grow | pH: 3.5 Details: CRYSTAL GREW FROM A SOLUTION OF 2%(V/V) 15% (W/V) PEG 1500, PH 3.5 | |||||||||||||||
Crystal | *PLUS | |||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion, sitting drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1997 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 21864 / % possible obs: 97 % / Observed criterion σ(I): -2 / Redundancy: 4 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 26.3 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.287 / % possible all: 77.6 |
Reflection | *PLUS Num. measured all: 87331 |
Reflection shell | *PLUS % possible obs: 77.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GAR Resolution: 1.8→50 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Details: RESIDUES 111 - 131 HAVE NO OBSERVABLE ELECTRON DENSITY AND ARE NOT INCLUDED IN THE FINAL MODEL. RESIDUES 141 - 145, AND 158 - 165 ARE LOCATED IN FLEXIBLE LOOPS AND HAVE HIGH B FACTORS.
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Displacement parameters | Biso mean: 25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.89 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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