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- PDB-2wag: The Structure of a family 25 Glycosyl hydrolase from Bacillus ant... -

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Basic information

Entry
Database: PDB / ID: 2wag
TitleThe Structure of a family 25 Glycosyl hydrolase from Bacillus anthracis.
ComponentsLYSOZYME, PUTATIVE
KeywordsHYDROLASE / GH25 / LYSIN / LYSOZYME / BACILLUS ANTHRACIS
Function / homology
Function and homology information


peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme activity / membrane
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
Biological speciesBACILLUS ANTHRACIS (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMartinez-Fleites, C. / Korczynska, J.E. / Cope, M. / Turkenburg, J.P. / Taylor, E.J.
CitationJournal: Carbohydr.Res. / Year: 2009
Title: The Crystal Structure of a Family Gh25 Lysozyme from Bacillus Anthracis Implies a Neighboring-Group Catalytic Mechanism with Retention of Anomeric Configuration
Authors: Martinez-Fleites, C. / Korczynska, J.E. / Cope, M. / Turkenburg, J.P. / Taylor, E.J.
History
DepositionFeb 6, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / reflns_shell
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf / _reflns_shell.Rmerge_I_obs
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-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: LYSOZYME, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,41814
Polymers26,0801
Non-polymers8,33813
Water6,702372
1
A: LYSOZYME, PUTATIVE
hetero molecules

A: LYSOZYME, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,83728
Polymers52,1612
Non-polymers16,67626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
Buried area3480 Å2
ΔGint-19.6 kcal/mol
Surface area23400 Å2
MethodPQS
Unit cell
Length a, b, c (Å)100.522, 100.521, 106.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 1 molecules A

#1: Protein LYSOZYME, PUTATIVE / FAMILY GH25 LYSOZYME


Mass: 26080.330 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 37-245
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS ANTHRACIS (anthrax bacterium) / Strain: AMES / Plasmid: YSBLLIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q81YN8, UniProt: A0A6L7H2K3*PLUS, lysozyme

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Non-polymers , 5 types, 385 molecules

#2: Chemical
ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


Mass: 1529.829 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE N-TERMINAL SIGNAL PEPTIDE, (SEQUENCE MKKKLFIRGIFILVSVMSVVAYLVFQGIFIPNQISA WAS REPLACED BY A ...THE N-TERMINAL SIGNAL PEPTIDE, (SEQUENCE MKKKLFIRGIFILVSVMSVVAYLVFQGIFIPNQISA WAS REPLACED BY A VECTOR DERIVED HEXAHISTIDINE TAG, (SEQUENCE MGSSHHHHHHM).

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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: 3.1 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5 / Details: 2.1M NH4 SO4, 0.1M TRIS PH 8.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.4→87 Å / Num. obs: 62904 / % possible obs: 99.9 % / Observed criterion σ(I): 6 / Redundancy: 16.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.4
Reflection shellResolution: 1.4→1.8 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 20 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.4.0077refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JFX

1jfx


Resolution: 1.4→33.73 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 0.832 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21217 3191 5.1 %RANDOM
Rwork0.18733 ---
obs0.18859 59675 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.423 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.03 Å20 Å2
2--0.06 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.4→33.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1815 0 71 372 2258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222177
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6141.9522949
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.235269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.49823.839112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9115394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1811513
X-RAY DIFFRACTIONr_chiral_restr0.3460.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021682
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_it1.1691.51225
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.86322005
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9783952
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1534.5933
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.68932177
X-RAY DIFFRACTIONr_sphericity_free4.973376
X-RAY DIFFRACTIONr_sphericity_bonded4.29632110
LS refinement shellResolution: 1.399→1.435 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 219 -
Rwork0.289 4294 -
obs--98.26 %

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