+Open data
-Basic information
Entry | Database: PDB / ID: 1d7b | ||||||||||||
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Title | CYTOCHROME DOMAIN OF CELLOBIOSE DEHYDROGENASE, PH 7.5 | ||||||||||||
Components | CELLOBIOSE DEHYDROGENASE | ||||||||||||
Keywords | OXIDOREDUCTASE / B-TYPE CYTOCHROME / MET/HIS LIGATION / BETA SANDWICH / FE(II)-PROTOPORPHYRIN IX | ||||||||||||
Function / homology | Function and homology information cellobiose dehydrogenase (acceptor) / cellobiose dehydrogenase (acceptor) activity / cellulose catabolic process / flavin adenine dinucleotide binding / extracellular region / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Phanerochaete chrysosporium (fungus) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å | ||||||||||||
Authors | Hallberg, B.M. / Bergfors, T. / Backbro, K. / Divne, C. | ||||||||||||
Citation | Journal: Structure Fold.Des. / Year: 2000 Title: A new scaffold for binding haem in the cytochrome domain of the extracellular flavocytochrome cellobiose dehydrogenase. Authors: Hallberg, B.M. / Bergfors, T. / Backbro, K. / Pettersson, G. / Henriksson, G. / Divne, C. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d7b.cif.gz | 91.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d7b.ent.gz | 73.7 KB | Display | PDB format |
PDBx/mmJSON format | 1d7b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d7b_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 1d7b_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 1d7b_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | 1d7b_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/1d7b ftp://data.pdbj.org/pub/pdb/validation_reports/d7/1d7b | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | THE BIOLOGICAL ASSEMBLY IS A MONOMERIC FLAVOCYTOCHROME CONSISTING OF A B-TYPE CYTOCHROME DOMAIN LINKED TO A FLAVODEHYDROGENASE DOMAIN. |
-Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 20012.768 Da / Num. of mol.: 2 / Fragment: CYTOCHROME TYPE B DOMAIN / Source method: isolated from a natural source / Source: (natural) Phanerochaete chrysosporium (fungus) / Tissue: SECRETED References: GenBank: 1314367, UniProt: Q01738*PLUS, EC: 1.1.3.25 #2: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 4 types, 335 molecules
#3: Chemical | ChemComp-CD / #4: Chemical | #5: Chemical | ChemComp-1PG / | #6: 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: 3.77 Å3/Da / Density % sol: 67.36 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 4000, 2-methyl-2,4-pentanediol, hepes, cadmium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: drop consists of equal amounts of protein and reservoir solutions | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.835 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.835 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25 Å / Num. all: 46876 / Num. obs: 46876 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 4 % / Rmerge(I) obs: 0.261 / Num. unique all: 2325 / % possible all: 98.8 |
Reflection | *PLUS Num. measured all: 168578 |
Reflection shell | *PLUS % possible obs: 98.8 % / Mean I/σ(I) obs: 5.4 |
-Processing
Software |
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Refinement | Resolution: 1.9→25 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER / Details: MAXIMUM LIKELIHOOD, BULK SOLVENT CORRECTION
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Refinement step | Cycle: LAST / Resolution: 1.9→25 Å
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Refine LS restraints |
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Software | *PLUS Name: 'CNS, SHELXL-97' / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 44889 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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