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- PDB-2brw: Crystal structure of Streptococcus Pneumoniae Hyaluronate Lyase f... -

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Basic information

Entry
Database: PDB / ID: 2brw
TitleCrystal structure of Streptococcus Pneumoniae Hyaluronate Lyase from 30percent PEGMME.
ComponentsHYALURONATE LYASE
KeywordsLYASE / (ALFA5/ALFA5) BARREL / CELL WALL / PEPTIDOGLYCAN-ANCHOR
Function / homology
Function and homology information


hyaluronate lyase / hyaluronate lyase activity / carbohydrate binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
Hyaluronate lyase, beta-sheet domain superfamily / : / Hyaluronate lyase, N-terminal beta-sheet domain / : / BppA domain 1 / Polysaccharide lyase 8 / Polysaccharide lyase 8, N-terminal alpha-helical / Polysaccharide lyase family 8, N terminal alpha-helical domain / Polysaccharide lyase family 8, C-terminal / Polysaccharide lyase family 8, C-terminal beta-sandwich domain ...Hyaluronate lyase, beta-sheet domain superfamily / : / Hyaluronate lyase, N-terminal beta-sheet domain / : / BppA domain 1 / Polysaccharide lyase 8 / Polysaccharide lyase 8, N-terminal alpha-helical / Polysaccharide lyase family 8, N terminal alpha-helical domain / Polysaccharide lyase family 8, C-terminal / Polysaccharide lyase family 8, C-terminal beta-sandwich domain / Polysaccharide lyase family 8, central domain / Polysaccharide lyase family 8, super-sandwich domain / Polysaccharide lyase family 8-like, C-terminal / Chondroitinase Ac; Chain A, domain 3 / Polysaccharide lyase family 8-like, C-terminal / Chondroitin AC/alginate lyase / Chondroitin AC/alginate lyase / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / Gram-positive cocci surface proteins LPxTG motif profile. / Glycosyltransferase / Alpha/alpha barrel / LPXTG cell wall anchor domain / Galactose-binding-like domain superfamily / Distorted Sandwich / Immunoglobulin E-set / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRigden, D.J. / Littlejohn, J.E. / Jedrzejas, M.J.
CitationJournal: J.Mol.Biol. / Year: 2006
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
DepositionMay 11, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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 viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HYALURONATE LYASE
B: HYALURONATE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,3164
Polymers167,1242
Non-polymers1922
Water2,018112
1
A: HYALURONATE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6582
Polymers83,5621
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: HYALURONATE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6582
Polymers83,5621
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)86.675, 84.061, 98.665
Angle α, β, γ (deg.)90.00, 98.87, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9999, 0.00593, -0.01314), (-0.00584, -0.99996, -0.00638), (-0.01318, -0.0063, 0.99989)
Vector: 50.8369, -17.81847, -48.31758)

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Components

#1: Protein HYALURONATE LYASE / HYALURONIDASE / HYASE


Mass: 83561.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q54873, hyaluronate lyase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE 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 DETAILING SEVERAL SEQUENCE CONFLICTS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 42.8 %
Crystal growpH: 6.5
Details: 30% POLYETHYLENE GLYCOL MONOMETHYL ETHER (PEGMME) 2000, 0.1 M MES BUFFER, PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1
DetectorType: OXFORD INSTRUMENTS / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
REFMAC5.2.0003refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EGU

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.
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1517 4.9 %RANDOM
Rwork0.229 ---
obs0.231 29209 88.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.87 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å20 Å20.03 Å2
2---1 Å20 Å2
3---2.53 Å2
Refinement stepCycle: LAST / Resolution: 2.8→95.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11582 0 10 112 11704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02211828
X-RAY DIFFRACTIONr_bond_other_d00.0210214
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.93715978
X-RAY DIFFRACTIONr_angle_other_deg3.614323968
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.39351440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.74925.205584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.191152134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9911550
X-RAY DIFFRACTIONr_chiral_restr0.1060.21716
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213182
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022356
X-RAY DIFFRACTIONr_nbd_refined0.240.23023
X-RAY DIFFRACTIONr_nbd_other0.270.210804
X-RAY DIFFRACTIONr_nbtor_refined0.1980.25928
X-RAY DIFFRACTIONr_nbtor_other0.1110.25725
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2411
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.257
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3570.2129
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3690.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.481.57164
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.529211572
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.48734664
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.2034.54406
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.95 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.384 238
Rwork0.317 4175

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