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- PDB-4ng1: Previously de-ionized HEW lysozyme batch crystallized in 1.9 M CsCl -

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Basic information

Entry
Database: PDB / ID: 4ng1
TitlePreviously de-ionized HEW lysozyme batch crystallized in 1.9 M CsCl
ComponentsLysozyme C
KeywordsHYDROLASE / Hofmeister series / protein cation interactions / 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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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 1, 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_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_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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_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)14,5003
Polymers14,3311
Non-polymers1682
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.435, 79.435, 38.115
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-342-

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 / Fragment: HEW LYSOZYME / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cs
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.1 Å3/Da / Density % sol: 41.36 %
Crystal growTemperature: 293 K / pH: 4.5
Details: Previously de-ionized lysozyme, no buffer added, 1.9 M CsCl, pH 4.5, Batch crystallization, temperature 293K

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: D41A / Wavelength: 1.388
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 1, 2000 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.388 Å / Relative weight: 1
ReflectionResolution: 1.82→34.36 Å / Num. obs: 11429 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 17 Å2 / Rsym value: 0.109 / Net I/σ(I): 12.7
Reflection shellResolution: 1.82→1.89 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.32 / % possible all: 100

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Processing

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

193l


Resolution: 1.82→56.17 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.683 / SU ML: 0.072 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18954 926 8.1 %RANDOM
Rwork0.15817 ---
obs0.16081 10471 99.82 %-
all-20870 --
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.6 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.955 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å2-0 Å2
2--0.09 Å20 Å2
3----0.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.82→56.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 2 83 1086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191067
X-RAY DIFFRACTIONr_bond_other_d0.0010.02987
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.9071445
X-RAY DIFFRACTIONr_angle_other_deg0.84732254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5835136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43622.74551
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81315179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8231512
X-RAY DIFFRACTIONr_chiral_restr0.090.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021256
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02282
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_it1.2290.856535
X-RAY DIFFRACTIONr_mcbond_other1.2020.852534
X-RAY DIFFRACTIONr_mcangle_it1.9341.281672
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.411.293532
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: 1.821→1.868 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 60 -
Rwork0.209 757 -
obs--99.88 %
Refinement TLS params.Method: refined / Origin x: 0.712 Å / Origin y: 58.871 Å / Origin z: 0.168 Å
111213212223313233
T0.0128 Å2-0.0055 Å2-0.003 Å2-0.0303 Å20.0165 Å2--0.0472 Å2
L2.0727 °2-1.1158 °2-0.1377 °2-2.1748 °20.3273 °2--1.4423 °2
S-0.0358 Å °-0.0135 Å °0.0535 Å °0.0491 Å °0.0389 Å °-0.1629 Å °-0.0442 Å °0.0677 Å °-0.0032 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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