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- PDB-3gxr: The crystal structure of g-type lysozyme from Atlantic cod (Gadus... -

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Basic information

Entry
Database: PDB / ID: 3gxr
TitleThe crystal structure of g-type lysozyme from Atlantic cod (Gadus morhua L.) in complex with NAG oligomers sheds new light on substrate binding and the catalytic mechanism. Structure with NAG to 1.7
ComponentsGoose-type lysozyme 1
KeywordsHYDROLASE / Atlantic cod / fish lysozyme / active site residues / substrate binding sites / surface potential / muramidase activity / immune system
Function / homology
Function and homology information


peptidoglycan catabolic process / lysozyme / lysozyme activity / defense response to Gram-positive bacterium / extracellular region
Similarity search - Function
Glycoside hydrolase, family 23 / Transglycosylase SLT domain / Lysozyme - #10 / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
triacetyl-beta-chitotriose / Lysozyme g
Similarity search - Component
Biological speciesGadus morhua (Atlantic cod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHelland, R. / Larsen, R.L. / Finstad, S. / Kyomuhendo, P. / Larsen, A.N.
CitationJournal: Cell.Mol.Life Sci. / Year: 2009
Title: Crystal structures of g-type lysozyme from Atlantic cod shed new light on substrate binding and the catalytic mechanism.
Authors: Helland, R. / Larsen, R.L. / Finstad, S. / Kyomuhendo, P. / Larsen, A.N.
History
DepositionApr 2, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Goose-type lysozyme 1
B: Goose-type lysozyme 1
C: Goose-type lysozyme 1
D: Goose-type lysozyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0569
Polymers83,3244
Non-polymers2,7325
Water5,278293
1
A: Goose-type lysozyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8833
Polymers20,8311
Non-polymers1,0522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Goose-type lysozyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4592
Polymers20,8311
Non-polymers6281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Goose-type lysozyme 1


Theoretical massNumber of molelcules
Total (without water)20,8311
Polymers20,8311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Goose-type lysozyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8833
Polymers20,8311
Non-polymers1,0522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.190, 75.520, 78.290
Angle α, β, γ (deg.)90.00, 93.25, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Goose-type lysozyme 1


Mass: 20831.008 Da / Num. of mol.: 4 / Fragment: UNP residues 31-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gadus morhua (Atlantic cod) / Gene: lysozyme / Plasmid: pET151/D-TOPO gLYS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: B9TU22, lysozyme
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE DISCREPANCY FROM THE DEPOSITED UNIPROT SEQUENCE IS DUE TO ALLELIC VARIATION OF THE GENE.

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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: 1.95 Å3/Da / Density % sol: 36.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 48-53% ammonium sulphate, 5mM CoCl2, 0.1M BisTris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 29, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.7→34 Å / Num. all: 70454 / Num. obs: 69961 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 22.34 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 7.8
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.353 / % possible all: 95.6

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
REFMAC5.4.0069refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GXK

3gxk


Resolution: 1.7→34 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.919 / SU B: 2.719 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25231 3525 5 %RANDOM
Rwork0.20369 ---
obs0.20611 66412 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.496 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å2-1.68 Å2
2---0.84 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.7→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5731 0 187 293 6211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0216043
X-RAY DIFFRACTIONr_angle_refined_deg1.8231.9578180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2355723
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89324.329298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.42715986
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9321540
X-RAY DIFFRACTIONr_chiral_restr0.1410.2891
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024595
X-RAY DIFFRACTIONr_mcbond_it1.1071.53594
X-RAY DIFFRACTIONr_mcangle_it1.82425759
X-RAY DIFFRACTIONr_scbond_it2.92432449
X-RAY DIFFRACTIONr_scangle_it4.4314.52421
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 257 -
Rwork0.257 4458 -
obs--91.91 %

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