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- PDB-2x8r: The structure of a family GH25 lysozyme from Aspergillus fumigatus -

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Basic information

Entry
Database: PDB / ID: 2x8r
TitleThe structure of a family GH25 lysozyme from Aspergillus fumigatus
ComponentsGLYCOSYL HYDROLASE
KeywordsHYDROLASE / PEPTIDOGLYCAN CLEAVAGE / ENDO-N-ACETYLMURAMIDASES / DXE MOTIF
Function / homology
Function and homology information


carbohydrate catabolic process / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to bacterium / extracellular region
Similarity search - Function
Glycoside hydrolase, family 25 subgroup / Glycosyl hydrolases family 25 / Glycoside hydrolase, family 25 / Glycosyl hydrolases family 25 / Glycosyl hydrolase family 25 (GH25) domain profile. / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
N,O-diacetylmuramidase
Similarity search - Component
Biological speciesASPERGILLUS FUMIGATUS (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKorczynska, J.E. / Danielsen, S. / Schagerlof, U. / Turkenburg, J.P. / Davies, G.J. / Wilson, K.S. / Taylor, E.J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: The Structure of a Family Gh25 Lysozyme from Aspergillus Fumigatus
Authors: Korczynska, J.E. / Danielsen, S. / Schagerlof, U. / Turkenburg, J.P. / Davies, G.J. / Wilson, K.S. / Taylor, E.J.
History
DepositionMar 11, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references / Refinement description / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN **-STRANDED BARREL THIS IS REPRESENTED BY A -9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -1-STRANDED BARREL THIS IS REPRESENTED BY A 0-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -1-STRANDED BARREL THIS IS REPRESENTED BY A 0-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -1-STRANDED BARREL THIS IS REPRESENTED BY A 0-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLYCOSYL HYDROLASE
B: GLYCOSYL HYDROLASE
C: GLYCOSYL HYDROLASE
D: GLYCOSYL HYDROLASE
E: GLYCOSYL HYDROLASE
F: GLYCOSYL HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,51712
Polymers140,3046
Non-polymers2136
Water20,3391129
1
A: GLYCOSYL HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4202
Polymers23,3841
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GLYCOSYL HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4202
Polymers23,3841
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: GLYCOSYL HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4202
Polymers23,3841
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: GLYCOSYL HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4202
Polymers23,3841
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: GLYCOSYL HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4202
Polymers23,3841
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: GLYCOSYL HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4202
Polymers23,3841
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.650, 111.720, 119.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
GLYCOSYL HYDROLASE / FAMILY 25 PEPTIDOGLYCAN HYDROLASE


Mass: 23384.047 Da / Num. of mol.: 6 / Fragment: RESIDUES 26-235 / Source method: isolated from a natural source / Source: (natural) ASPERGILLUS FUMIGATUS (mold) / Strain: AF293 / References: UniProt: A4DA29, lysozyme
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1129 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 Å3/Da / Density % sol: 37 % / Description: NONE
Crystal growpH: 4
Details: 0.1 M MIB SYSTEM (MALONIC ACID, IMIDAZOLE, BORIC ACID SYSTEM) PH 4.0 AND 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.7→40.57 Å / Num. obs: 118667 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.6.0056refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JFX

1jfx


Resolution: 1.7→81.5 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.209 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.20741 5938 5 %RANDOM
Rwork0.16896 ---
obs0.17094 112645 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.466 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20 Å2
2---0.32 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.7→81.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9814 0 6 1129 10949
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02110443
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.90514245
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.60351329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85323.708480
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.762151582
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7441542
X-RAY DIFFRACTIONr_chiral_restr0.1220.21434
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218260
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 434 -
Rwork0.254 8162 -
obs--99.14 %

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