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- PDB-2brw: Crystal structure of Streptococcus Pneumoniae Hyaluronate Lyase f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2brw | ||||||
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Title | Crystal structure of Streptococcus Pneumoniae Hyaluronate Lyase from 30percent PEGMME. | ||||||
![]() | HYALURONATE LYASE | ||||||
![]() | LYASE / (ALFA5/ALFA5) BARREL / CELL WALL / PEPTIDOGLYCAN-ANCHOR | ||||||
Function / homology | ![]() hyaluronate lyase / hyaluronate lyase activity / : / hydrolase activity, acting on glycosyl bonds / carbohydrate binding / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rigden, D.J. / Littlejohn, J.E. / Jedrzejas, M.J. | ||||||
![]() | ![]() Title: Alternate Structural Conformations of Streptococcus Pneumoniae Hyaluronan Lyase: Insights Into Enzyme Flexibility and Underlying Molecular Mechanism of Action. Authors: Rigden, D.J. / Littlejohn, J.E. / Joshi, H.V. / De Groot, B.L. / Jedrzejas, M.J. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 293.8 KB | Display | ![]() |
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PDB format | ![]() | 236.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.8 KB | Display | ![]() |
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Full document | ![]() | 494 KB | Display | |
Data in XML | ![]() | 54.3 KB | Display | |
Data in CIF | ![]() | 73.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2brvC ![]() 1eguS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9999, 0.00593, -0.01314), Vector: |
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Components
#1: Protein | Mass: 83561.938 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE SIX RESIDUE HIS TAG (RESIDUES A893-A898 AND B893-B898) WERE NOT SEEN IN THE DENSITY. THE ...THE SIX RESIDUE HIS TAG (RESIDUES A893-A898 AND B893-B898) WERE NOT SEEN IN THE DENSITY. THE UNIPROT ENTRY INCLUDES REFERENCES | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 42.8 % |
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Crystal grow | pH: 6.5 Details: 30% POLYETHYLENE GLYCOL MONOMETHYL ETHER (PEGMME) 2000, 0.1 M MES BUFFER, PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: OXFORD INSTRUMENTS / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→95.35 Å / Num. obs: 45379 / % possible obs: 87.3 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.4→2.47 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.2 / % possible all: 78.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1EGU Resolution: 2.8→95.35 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.832 / Cross valid method: THROUGHOUT / ESU R Free: 0.52 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.87 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→95.35 Å
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Refine LS restraints |
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