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Yorodumi- PDB-5ihp: Crystal Structure of Cobyrinic Acid a,c-diamide synthase from Myc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ihp | ||||||
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Title | Crystal Structure of Cobyrinic Acid a,c-diamide synthase from Mycobacterium smegmatis with bound ADP and Magnesium | ||||||
Components | Cobyrinic Acid a,c-diamide synthase | ||||||
Keywords | LIGASE / SSGCID / COBYRINIC ACID A / C-DIAMIDE SYNTHASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycobacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal Structure of Cobyrinic Acid a,c-diamide synthase from Mycobacterium smegmatis with bound ATP analog and Magnesium Authors: Davies, D.R. / Horanyi, P.S. / Abendroth, J.A. / SSGCID | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ihp.cif.gz | 202.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ihp.ent.gz | 159.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ihp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/5ihp ftp://data.pdbj.org/pub/pdb/validation_reports/ih/5ihp | HTTPS FTP |
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-Related structure data
Related structure data | 5if9C 4pfsS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 29410.924 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_1927 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QTQ5 #2: Chemical | #3: Chemical | #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: 2.01 Å3/Da / Density % sol: 38.92 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: EBS INTERNAL TRACKING NUMBER 500 MM NACL, 2 MM DTT, 0.025% SODIUM AZIDE, 5% GLYCEROL, 0.4 UL X 0.4 UL DROP WITH JCSG SCREEN CONDITION F3: 20% (V/V) MPD, 100 MM TRIS PH 8.0; 3 DAY SOAK WITH 5 ...Details: EBS INTERNAL TRACKING NUMBER 500 MM NACL, 2 MM DTT, 0.025% SODIUM AZIDE, 5% GLYCEROL, 0.4 UL X 0.4 UL DROP WITH JCSG SCREEN CONDITION F3: 20% (V/V) MPD, 100 MM TRIS PH 8.0; 3 DAY SOAK WITH 5 MM ADP + 5 MM MGCL2; 20% ETHYLENE GLYCOL CRYOPROTECTANT PH range: 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 30, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→42 Å / Num. obs: 41651 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 12.07 % / Biso Wilson estimate: 30.38 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 29.11 |
Reflection shell | Resolution: 1.85→1.9 Å / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 4.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PFS Resolution: 1.85→41.63 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 28.94 Å2 | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→41.63 Å
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