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- PDB-4ngz: Previously de-ionized HEW lysozyme crystallized in 0.5 M YbCl3/30... -

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Basic information

Entry
Database: PDB / ID: 4ngz
TitlePreviously de-ionized HEW lysozyme crystallized in 0.5 M YbCl3/30% (v/v) glycerol and collected at 125K
ComponentsLysozyme C
KeywordsHYDROLASE / Hofmeister series / protein cation interactions / HEW lysozyme / ESI-mass spectrometry
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
YTTERBIUM (III) ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBenas, P. / Legrand, L. / Ries-Kautt, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Weak protein-cationic co-ion interactions addressed by X-ray crystallography and mass spectrometry.
Authors: Benas, P. / Auzeil, N. / Legrand, L. / Brachet, F. / Regazzetti, A. / Ries-Kautt, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Strong and specific effects of cations on lysozyme chloride solubility.
Authors: Benas, P. / Legrand, L. / Ries-Kautt, M.
History
DepositionNov 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Sep 20, 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 / 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 / _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_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.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_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_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
Revision 1.5Nov 20, 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)14,9577
Polymers14,3311
Non-polymers6256
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.589, 78.589, 37.017
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-202-

YB

21A-379-

HOH

31A-380-

HOH

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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.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-YB / YTTERBIUM (III) ION


Mass: 173.040 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Yb
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 129 / 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: 1.99 Å3/Da / Density % sol: 38.32 %
Crystal growTemperature: 293 K / pH: 4.5
Details: Previously de-ionized lysozyme, no buffer added, 0.5 M YbCl3, 30% (v/v) glycerol , pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 125 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 17, 2000
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→19.65 Å / Num. obs: 13242 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Biso Wilson estimate: 20.1 Å2 / Rsym value: 0.067 / Net I/σ(I): 23.3
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.202 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
TRUNCATEdata scaling
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 193L

193l


Resolution: 1.7→55.57 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.669 / SU ML: 0.067 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20515 1241 9.4 %RANDOM
Rwork0.17824 ---
obs0.18081 11957 99.51 %-
all-21872 --
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.5 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.581 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å2-0 Å2
2--0.51 Å20 Å2
3----1.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→55.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 6 129 1136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191075
X-RAY DIFFRACTIONr_bond_other_d0.0020.02970
X-RAY DIFFRACTIONr_angle_refined_deg1.2961.9071430
X-RAY DIFFRACTIONr_angle_other_deg0.86132207
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3795132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.81822.88552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76315172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.711512
X-RAY DIFFRACTIONr_chiral_restr0.0870.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021249
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02281
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_it1.3741.302528
X-RAY DIFFRACTIONr_mcbond_other1.3181.292526
X-RAY DIFFRACTIONr_mcangle_it1.9071.94660
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.381.637546
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
Rfree0.321 82 -
Rwork0.26 849 -
obs--97.18 %
Refinement TLS params.Method: refined / Origin x: 0.969 Å / Origin y: 58.363 Å / Origin z: 0.662 Å
111213212223313233
T0.0238 Å20.0032 Å20.0068 Å2-0.0308 Å2-0.0027 Å2--0.0188 Å2
L1.3921 °2-0.873 °20.1722 °2-1.6645 °20.2733 °2--0.9653 °2
S-0.027 Å °0.0133 Å °0.0697 Å °0.0503 Å °0.0566 Å °-0.1463 Å °-0.0201 Å °0.0706 Å °-0.0296 Å °
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3BPion.paramBPion.top

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