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Yorodumi- PDB-1avd: THREE-DIMENSIONAL STRUCTURE OF THE TETRAGONAL CRYSTAL FORM OF EGG... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1avd | ||||||
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Title | THREE-DIMENSIONAL STRUCTURE OF THE TETRAGONAL CRYSTAL FORM OF EGG-WHITE AVIDIN IN ITS FUNCTIONAL COMPLEX WITH BIOTIN AT 2.7 ANGSTROMS RESOLUTION | ||||||
Components | AVIDIN | ||||||
Keywords | BIOTIN-BINDING PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.7 Å | ||||||
Authors | Pugliese, L. / Coda, A. / Malcovati, M. / Bolognesi, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1993 Title: Three-dimensional structure of the tetragonal crystal form of egg-white avidin in its functional complex with biotin at 2.7 A resolution. Authors: Pugliese, L. / Coda, A. / Malcovati, M. / Bolognesi, M. #1: Journal: To be Published Title: Crystal Structure of Hen Egg-White Apo-Avidin in Relation to its Thermal Stability Properties Authors: Pugliese, L. / Malcovati, M. / Coda, A. / Bolognesi, M. #2: Journal: J.Mol.Biol. / Year: 1984 Title: Crystallization of Hen Egg-White Avidin in a Tetragonal Form Authors: Gatti, G. / Bolognesi, M. / Coda, A. / Chiolerio, F. / Filippini, E. / Malcovati, M. | ||||||
History |
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Remark 700 | SHEET THE SHEET PRESENTED AS *CH1* ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT-STRANDED BETA-BARREL. ...SHEET THE SHEET PRESENTED AS *CH1* ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT-STRANDED BETA-BARREL. THIS IS REPRESENTED BY A NINE-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1avd.cif.gz | 59 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1avd.ent.gz | 47.5 KB | Display | PDB format |
PDBx/mmJSON format | 1avd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/1avd ftp://data.pdbj.org/pub/pdb/validation_reports/av/1avd | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.5282, 0.849, -0.009), Vector: Details | THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. | |
-Components
#1: Protein | Mass: 14350.081 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / References: UniProt: P02701 #2: Sugar | ChemComp-NAG / | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | POSITION 34 SHOWS RESIDUE MICROHETEROGENEITY (THR OR ILE), AS DETERMINED FROM AMINO ACID SEQUENCING. ...POSITION 34 SHOWS RESIDUE MICROHETER | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.44 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 5.7 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Num. obs: 8087 / Num. measured all: 69005 / Rmerge(I) obs: 0.129 |
-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.174 / Highest resolution: 2.7 Å | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.7 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 10 Å / Num. reflection obs: 7255 / Rfactor obs: 0.174 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 3 Å |