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Yorodumi- PDB-1zrq: Escherichia coli Methylenetetrahydrofolate Reductase (reduced) co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zrq | ||||||
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Title | Escherichia coli Methylenetetrahydrofolate Reductase (reduced) complexed with NADH, pH 6.0 | ||||||
Components | 5,10-methylenetetrahydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE / TIM BARREL / FLAVIN / REDUCTASE / NADH | ||||||
Function / homology | Function and homology information methylenetetrahydrofolate reductase [NAD(P)H] / methylenetetrahydrofolate reductase (NADPH) activity / methylenetetrahydrofolate reductase (NADH) / methylenetetrahydrofolate reductase (NADH) activity / methylenetetrahydrofolate reductase (NAD(P)H) activity / methionine biosynthetic process / tetrahydrofolate interconversion / FAD binding / protein-folding chaperone binding / protein-containing complex / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Pejchal, R. / Sargeant, R. / Ludwig, M.L. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Structures of NADH and CH(3)-H(4)Folate Complexes of Escherichia coli Methylenetetrahydrofolate Reductase Reveal a Spartan Strategy for a Ping-Pong Reaction Authors: Pejchal, R. / Sargeant, R. / Ludwig, M.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zrq.cif.gz | 186 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zrq.ent.gz | 147.7 KB | Display | PDB format |
PDBx/mmJSON format | 1zrq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zrq_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 1zrq_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 1zrq_validation.xml.gz | 37.3 KB | Display | |
Data in CIF | 1zrq_validation.cif.gz | 49.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/1zrq ftp://data.pdbj.org/pub/pdb/validation_reports/zr/1zrq | HTTPS FTP |
-Related structure data
Related structure data | 1zp3C 1zp4C 1zptC 1b5tS 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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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 34215.852 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: metF / Plasmid: pET23B / Production host: Escherichia coli (E. coli) References: UniProt: P00394, UniProt: P0AEZ1*PLUS, EC: 1.7.99.5 #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | #5: 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: 2.69 Å3/Da / Density % sol: 54.2 % |
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Crystal grow | Temperature: 295 K / pH: 6 Details: PEG 4000, LITHIUM SULFATE, SODIUM CACODYLATE, ETHANOL, MESO-ERYTHRITOL, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K, pH 6.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 1 / Detector: CCD / Date: May 23, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 54123 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 2.34 % / Biso Wilson estimate: 26.1 Å2 / Rsym value: 0.065 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.2→2.28 Å / Mean I/σ(I) obs: 2.8 / Rsym value: 0.274 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1B5T Resolution: 2.2→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2239424.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.72 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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