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Yorodumi- PDB-2p4t: Structure of the Q67H mutant of R67 dihydrofolate reductase-NADP+... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2p4t | ||||||
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Title | Structure of the Q67H mutant of R67 dihydrofolate reductase-NADP+ complex reveals a novel cofactor binding mode | ||||||
Components | Dihydrofolate reductase type 2 | ||||||
Keywords | OXIDOREDUCTASE / bacterial infections / folate metabolism / NADP+ / R67 DHFR / Symmetric binding / trimethoprim-resistance | ||||||
Function / homology | Function and homology information response to methotrexate / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / response to xenobiotic stimulus / response to antibiotic Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å | ||||||
Authors | Divya, N. / Grifith, E. / Narayana, N. | ||||||
Citation | Journal: Protein Sci. / Year: 2007 Title: Structure of the Q67H mutant of R67 dihydrofolate reductase-NADP+ complex reveals a novel cofactor binding mode. Authors: Divya, N. / Grifith, E. / Narayana, N. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2006 Title: High-resolution structure of a plasmid-encoded dihydrofolate reductase: pentagonal network of water molecules in the D2-symmetric active site Authors: Narayana, N. #2: Journal: Nat.Struct.Biol. / Year: 1995 Title: A Plasmid-Encoded Dihydrofolate Reductase from Trimethoprim-Resistant Bacteria has a Novel D2-Symmetric Active Site Authors: Narayana, N. / Matthews, D.A. / Howell, E.E. / Xuong, N. #3: Journal: Protein Eng. / Year: 1997 Title: A glutamine 67-->histidine mutation in homotetrameric R67 dihydrofolate reductase results in four mutations per single active site pore and causes substantial substrate and cofactor inhibition Authors: Park, H. / Bradrick, T.D. / Howell, E.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p4t.cif.gz | 28.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p4t.ent.gz | 17.1 KB | Display | PDB format |
PDBx/mmJSON format | 2p4t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/2p4t ftp://data.pdbj.org/pub/pdb/validation_reports/p4/2p4t | HTTPS FTP |
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-Related structure data
Related structure data | 1vieS S: Starting model for refinement |
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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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Details | The biological assembly is comprised of four subunits generated by symmetry axes. The crystallographic 222 symmetry generates the biologically active tetramer. x,y,z; -x+1,-y+1,z; y,x,-z+1; -y+1,-x+1,-z+1 |
-Components
#1: Protein | Mass: 6742.546 Da / Num. of mol.: 1 / Mutation: Residues 1-16 are cleaved and Q67H mutation Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Strain: TMP-RESISTANT, CONTAINING R67 DHFR OVERPRODUCING PLASMID PLZ1 Production host: Escherichia coli (E. coli) / References: UniProt: P00383, dihydrofolate reductase |
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#2: Chemical | ChemComp-NAP / |
#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: 2.23 Å3/Da / Density % sol: 44.81 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Tris-Hcl buffer, 20% PEG1000 and 10% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 23, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→20 Å / Num. all: 19048 / Num. obs: 18488 / % possible obs: 86.6 % / Observed criterion σ(I): 1 / Redundancy: 7.1 % / Rsym value: 0.039 / Net I/σ(I): 30.2 |
Reflection shell | Resolution: 1.15→1.24 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 1609 / Rsym value: 0.285 / % possible all: 60.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1VIE Resolution: 1.15→20 Å / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber Details: HOH 149 HAS PARTIAL OCCUPANCY. WHEN COFACTOR IS BOUND, THE HOH 149 IS ABSENT. HOH 146 ALSO HAS PARTIAL OCCUPANCY.THE ADENOSINE PHOSPHATE PORTION OF THE COFACTOR IS NOT SEEN IN THE DENSITY. ...Details: HOH 149 HAS PARTIAL OCCUPANCY. WHEN COFACTOR IS BOUND, THE HOH 149 IS ABSENT. HOH 146 ALSO HAS PARTIAL OCCUPANCY.THE ADENOSINE PHOSPHATE PORTION OF THE COFACTOR IS NOT SEEN IN THE DENSITY. THEREFORE, THE RESPECTIVE ATOMIC COORDINATES ARE MISSING IN THIS LIST.
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Refinement step | Cycle: LAST / Resolution: 1.15→20 Å
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LS refinement shell | Resolution: 1.15→1.24 Å
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