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- PDB-2fbb: Crystal Structure Analysis of Hexagonal Lysozyme -

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Basic information

Entry
Database: PDB / ID: 2fbb
TitleCrystal Structure Analysis of Hexagonal Lysozyme
ComponentsLysozyme C
KeywordsHYDROLASE / hexagonal lysozyme
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsBrinkmann, C. / Weiss, M.S. / Weckert, E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: The structure of the hexagonal crystal form of hen egg-white lysozyme.
Authors: Brinkmann, C. / Weiss, M.S. / Weckert, E.
History
DepositionDec 9, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / 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 / _diffrn_source.pdbx_synchrotron_site / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,43822
Polymers14,3311
Non-polymers1,10721
Water2,972165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.637, 85.637, 67.932
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-132-

NA

21A-133-

NA

31A-150-

NO3

41A-150-

NO3

51A-158-

NO3

61A-158-

NO3

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Components

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


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.51 Å3/Da / Density % sol: 50.97 %
Crystal growTemperature: 293 K / pH: 8.4
Details: 10% aqu. acetone solution saturated with sodium nitrate, 25mg/ml lysozyme, pH 8.4, batch, temperature 293.0K, pH 8.40

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Data collection

DiffractionMean temperature: 10 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8043
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 30, 2004
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8043 Å / Relative weight: 1
ReflectionResolution: 1.46→70 Å / Num. obs: 25570 / % possible obs: 100 % / Observed criterion σ(I): 3.5 / Redundancy: 23 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 77.6
Reflection shellResolution: 1.46→1.47 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.884 / Mean I/σ(I) obs: 3.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DPW.pdb

1dpw


Resolution: 1.46→70 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.474 / SU ML: 0.049 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.198 528 2.1 %RANDOM
Rwork0.183 ---
obs0.183 25016 98.1 %-
all-26041 --
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: 27.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0.07 Å20 Å2
2---0.14 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.46→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 69 165 1235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0211088
X-RAY DIFFRACTIONr_bond_other_d0.0020.02890
X-RAY DIFFRACTIONr_angle_refined_deg1.981.9431456
X-RAY DIFFRACTIONr_angle_other_deg1.02732063
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.1065128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.34723.26952
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5515169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9411511
X-RAY DIFFRACTIONr_chiral_restr0.1330.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021252
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02229
X-RAY DIFFRACTIONr_nbd_refined0.2490.2263
X-RAY DIFFRACTIONr_nbd_other0.2040.21014
X-RAY DIFFRACTIONr_nbtor_refined0.1890.2532
X-RAY DIFFRACTIONr_nbtor_other0.090.2600
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3030.2111
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1690.212
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5270.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3110.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3440.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2110.24
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4191.5691
X-RAY DIFFRACTIONr_mcbond_other0.3891.5270
X-RAY DIFFRACTIONr_mcangle_it1.72721014
X-RAY DIFFRACTIONr_scbond_it2.6223424
X-RAY DIFFRACTIONr_scangle_it4.014.5442
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.46→1.5 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 26 -
Rwork0.204 1844 -
obs--99.1 %
Refinement TLS params.Method: refined / Origin x: 27.2153 Å / Origin y: 2.6081 Å / Origin z: 19.3633 Å
111213212223313233
T-0.2131 Å2-0.0048 Å20.0491 Å2--0.0624 Å2-0.0898 Å2---0.1188 Å2
L4.062 °20.5248 °21.0697 °2-1.1078 °20.3321 °2--2.455 °2
S0.0945 Å °0.0195 Å °0.1299 Å °-0.1238 Å °-0.0127 Å °-0.0933 Å °-0.0539 Å °0.4063 Å °-0.0818 Å °

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