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Yorodumi- PDB-4nm9: Crystal structure of the resting state of proline utilization A (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nm9 | ||||||
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Title | Crystal structure of the resting state of proline utilization A (PutA) from Geobacter sulfurreducens PCA | ||||||
Components | Proline dehydrogenase and Delta-1-pyrroline-5-carboxylate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / flavoenzyme / Rossmann fold / aldehyde dehydrogenase / flavin adenine dinucleotide / nicotinamide adenine dinucleotide / proline catabolism / substrate channeling / bifunctional enzyme | ||||||
Function / homology | Function and homology information proline dehydrogenase activity / L-glutamate gamma-semialdehyde dehydrogenase / 1-pyrroline-5-carboxylate dehydrogenase activity / proline catabolic process to glutamate / cytoplasmic side of plasma membrane / DNA-binding transcription factor activity / nucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | Geobacter sulfurreducens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.898 Å | ||||||
Authors | Singh, H. / Tanner, J.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Structures of the PutA peripheral membrane flavoenzyme reveal a dynamic substrate-channeling tunnel and the quinone-binding site. Authors: Singh, H. / Arentson, B.W. / Becker, D.F. / Tanner, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nm9.cif.gz | 771.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nm9.ent.gz | 627.3 KB | Display | PDB format |
PDBx/mmJSON format | 4nm9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nm9_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4nm9_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4nm9_validation.xml.gz | 75.2 KB | Display | |
Data in CIF | 4nm9_validation.cif.gz | 111.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nm/4nm9 ftp://data.pdbj.org/pub/pdb/validation_reports/nm/4nm9 | HTTPS FTP |
-Related structure data
Related structure data | 4nmaC 4nmbC 4nmcSC 4nmdC 4nmeC 4nmfC C: citing same article (ref.) 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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-Components
#1: Protein | Mass: 112324.672 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Strain: ATCC 51573 / DSM 12127 / PCA / Gene: putA, GSU3395 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI References: UniProt: Q746X3, EC: 1.5.99.8, EC: 1.5.1.12, L-glutamate gamma-semialdehyde dehydrogenase #2: Chemical | #3: Chemical | ChemComp-EDO / #4: 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: 2.81 Å3/Da / Density % sol: 56.18 % |
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Crystal grow | Temperature: 298 K / Method: microbatch / pH: 6.5 Details: 25-28% PEG550 MME, 0.05-0.15 M Bis-Tris, pH 6.3-6.5, 0.05 M calcium chloride, MICROBATCH, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Cryo-Cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.898→49.052 Å / Num. all: 197435 / Num. obs: 197435 / % possible obs: 99.1 % / Redundancy: 4.6 % / Biso Wilson estimate: 23.93 Å2 / Rsym value: 0.076 / Net I/σ(I): 13 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4NMC Resolution: 1.898→49.052 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.883 / SU ML: 0.19 / σ(F): 1.35 / Phase error: 19.06 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.41 Å2 / Biso mean: 21.4845 Å2 / Biso min: 8.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.898→49.052 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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