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Yorodumi- PDB-4au1: Crystal Structure of CobH (precorrin-8x methyl mutase) complexed ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4au1 | ||||||
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Title | Crystal Structure of CobH (precorrin-8x methyl mutase) complexed with C5 desmethyl-HBA | ||||||
Components | PRECORRIN-8X METHYLMUTASE | ||||||
Keywords | ISOMERASE / PRECORRIN / HBA | ||||||
Function / homology | Function and homology information precorrin-8X methylmutase / precorrin-8X methylmutase activity / cobalamin biosynthetic process Similarity search - Function | ||||||
Biological species | RHODOBACTER CAPSULATUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Deery, E. / Lawrence, A.D. / Schroeder, S. / Taylor, S.L. / Seyedarabi, A. / Vevodova, J. / Wilson, K.S. / Brown, D. / Geeves, M.A. / Howard, M.J. ...Deery, E. / Lawrence, A.D. / Schroeder, S. / Taylor, S.L. / Seyedarabi, A. / Vevodova, J. / Wilson, K.S. / Brown, D. / Geeves, M.A. / Howard, M.J. / Pickersgill, R.W. / Warren, M.J. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2012 Title: An Enzyme-Trap Approach Allows Isolation of Intermediates in Cobalamin Biosynthesis Authors: Deery, E. / Schroeder, S. / Lawrence, A.D. / Taylor, S.L. / Seyedarabi, A. / Waterman, J. / Wilson, K.S. / Brown, D. / Geeves, M.A. / Howard, M.J. / Pickersgill, R.W. / Warren, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4au1.cif.gz | 102.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4au1.ent.gz | 78.2 KB | Display | PDB format |
PDBx/mmJSON format | 4au1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4au1_validation.pdf.gz | 1014.9 KB | Display | wwPDB validaton report |
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Full document | 4au1_full_validation.pdf.gz | 1015.7 KB | Display | |
Data in XML | 4au1_validation.xml.gz | 13 KB | Display | |
Data in CIF | 4au1_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/4au1 ftp://data.pdbj.org/pub/pdb/validation_reports/au/4au1 | HTTPS FTP |
-Related 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: 24188.016 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RHODOBACTER CAPSULATUS (bacteria) / Strain: SB1003 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: D5AV08, precorrin-8X methylmutase | ||
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#2: Chemical | ChemComp-P8X / | ||
#3: Chemical | ChemComp-SO4 / | ||
#4: Water | ChemComp-HOH / | ||
Nonpolymer details | C5 DES METHYL HBA (P8X): ALSO C15 APPEARS TO BE SP3 CF PREVIOUSLYSequence details | GENBANK ENTRY RCAP_RCC02046 | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.86 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 2, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→47.79 Å / Num. obs: 37503 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 19.09 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 1.45→1.49 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.2 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→47.79 Å / Cor.coef. Fo:Fc: 0.9672 / Cor.coef. Fo:Fc free: 0.9628 / SU R Cruickshank DPI: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.062 / SU Rfree Blow DPI: 0.061 / SU Rfree Cruickshank DPI: 0.058
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Displacement parameters | Biso mean: 21.13 Å2
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Refine analyze | Luzzati coordinate error obs: 0.154 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→47.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.49 Å / Total num. of bins used: 19
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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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