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- PDB-3wl2: Monoclinic Lysozyme at 0.96 A resolution -

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Basic information

Entry
Database: PDB / ID: 3wl2
TitleMonoclinic Lysozyme at 0.96 A resolution
ComponentsLysozyme C
KeywordsHYDROLASE
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily ...Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NITRATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 0.96 Å
AuthorsMatsumoto, T. / Yamano, A. / Hasegawa, T. / Maeyama, M.
CitationJournal: To be Published
Title: Evaluation of Rigaku XtaLAB P200
Authors: Matsumoto, T. / Yamano, A. / Hasegawa, T. / Maeyama, M.
History
DepositionNov 6, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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.ptnr2_auth_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme C
B: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,39015
Polymers28,6622
Non-polymers72813
Water6,792377
1
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,91211
Polymers14,3311
Non-polymers58110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4784
Polymers14,3311
Non-polymers1473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.353, 62.563, 60.090
Angle α, β, γ (deg.)90.00, 90.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14331.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 1.79 Å3/Da / Density % sol: 31.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.7
Details: 50mM Sodium Acetate pH4.7, 20% Ethylene glycol, 0.4M Sodium nitrate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Sep 6, 2013
RadiationMonochromator: VariMaxDW / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 0.96→30.045 Å / Num. all: 123121 / Num. obs: 111914 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.054
Reflection shellHighest resolution: 0.96 Å

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREP11.1.03phasing
REFMAC5.8.0049refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.96→30.045 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.271 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.027 / ESU R Free: 0.03
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19532 5621 5 %RANDOM
Rwork0.1596 ---
obs0.16138 106293 90.89 %-
all-111914 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.258 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0 Å20.05 Å2
2--0.02 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 0.96→30.045 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2000 0 46 377 2423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0192081
X-RAY DIFFRACTIONr_bond_other_d0.0010.021885
X-RAY DIFFRACTIONr_angle_refined_deg1.9141.9132806
X-RAY DIFFRACTIONr_angle_other_deg2.32934291
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9285256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80723100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59115332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.451522
X-RAY DIFFRACTIONr_chiral_restr0.1380.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022444
X-RAY DIFFRACTIONr_gen_planes_other0.010.02542
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_it4.3071.5491030
X-RAY DIFFRACTIONr_mcbond_other4.3051.5451029
X-RAY DIFFRACTIONr_mcangle_it4.0392.3261284
X-RAY DIFFRACTIONr_mcangle_other4.0372.3281285
X-RAY DIFFRACTIONr_scbond_it5.1711.8831051
X-RAY DIFFRACTIONr_scbond_other5.1711.8831051
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7322.7031523
X-RAY DIFFRACTIONr_long_range_B_refined6.15815.9173086
X-RAY DIFFRACTIONr_long_range_B_other5.92315.062908
X-RAY DIFFRACTIONr_rigid_bond_restr9.12133966
X-RAY DIFFRACTIONr_sphericity_free27.433571
X-RAY DIFFRACTIONr_sphericity_bonded15.77654237
LS refinement shellResolution: 0.96→0.985 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 382 -
Rwork0.247 7377 -
obs--85.45 %

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