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Yorodumi- PDB-3h7a: CRYSTAL STRUCTURE OF SHORT-CHAIN DEHYDROGENASE FROM Rhodopseudomo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3h7a | ||||||
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Title | CRYSTAL STRUCTURE OF SHORT-CHAIN DEHYDROGENASE FROM Rhodopseudomonas palustris | ||||||
Components | short chain dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / DEHYDROGENASE / PSI-2 / NYSGXRC / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS | ||||||
Function / homology | short chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Unknown ligand / Possible short chain dehydrogenase Function and homology information | ||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.87 Å | ||||||
Authors | Patskovsky, Y. / Toro, R. / Morano, C. / Freeman, J. / Miller, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: CRYSTAL STRUCTURE OF SHORT-CHAIN DEHYDROGENASE FROM Rhodopseudomonas palustris Authors: Patskovsky, Y. / Toro, R. / Morano, C. / Miller, S. / Freeman, J. / Sauder, J.M. / Burley, S.K. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3h7a.cif.gz | 181.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h7a.ent.gz | 145.7 KB | Display | PDB format |
PDBx/mmJSON format | 3h7a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3h7a_validation.pdf.gz | 463.4 KB | Display | wwPDB validaton report |
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Full document | 3h7a_full_validation.pdf.gz | 471 KB | Display | |
Data in XML | 3h7a_validation.xml.gz | 34.7 KB | Display | |
Data in CIF | 3h7a_validation.cif.gz | 50.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h7/3h7a ftp://data.pdbj.org/pub/pdb/validation_reports/h7/3h7a | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 27423.242 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Gene: RPA0021 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NDT3 #2: Chemical | Num. of mol.: 3 / Source method: obtained synthetically #3: 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: 2.59 Å3/Da / Density % sol: 52.62 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M CITRIC ACID PH 5.5, 20% PEG3350, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 21, 2009 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→50 Å / Num. obs: 95778 / % possible obs: 96.7 % / Observed criterion σ(I): -0.5 / Redundancy: 2.9 % / Rsym value: 0.132 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 1.87→1.94 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 0.8 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.87→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.704 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.773 Å2
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Refinement step | Cycle: LAST / Resolution: 1.87→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1555 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.87→1.918 Å / Total num. of bins used: 20
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