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- PDB-4bap: Hen egg-white lysozyme structure in complex with the europium tri... -

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Basic information

Entry
Database: PDB / ID: 4bap
TitleHen egg-white lysozyme structure in complex with the europium tris- hydroxyethylcholinetriazoledipicolinate complex at 1.21 A resolution.
ComponentsLYSOZYME C
KeywordsHYDROLASE / CLICK-CHEMISTRY / ANOMALOUS SCATTERING / DE NOVO PHASING / EXPERIMENTAL PHASING / LANTHANIDE COMPLEX / DIPICOLINATE
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
ACETATE ION / Chem-DCJ / EUROPIUM (III) ION / Lysozyme C
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.207 Å
AuthorsTalon, R. / Kahn, R. / Gautier, A. / Nauton, L. / Girard, E.
Citation
Journal: Chem.Commun.(Camb.) / Year: 2012
Title: Clicked Europium Dipicolinate Complexes for Protein X-Ray Structure Determination.
Authors: Talon, R. / Nauton, L. / Canet, J.-L. / Kahn, R. / Girard, E. / Gautier, A.
#1: Journal: Angew.Chem.Int.Ed.Engl. / Year: 2008
Title: Protein Crystallography Through Supramolecular Interactions between a Lanthanide Complex and Arginine.
Authors: Pompidor, G. / D'Aleo, A. / Vicat, J. / Toupet, L. / Giraud, N. / Kahn, R. / Maury, O.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2010
Title: A Dipicolinate Lanthanide Complex for Solving Protein Structures Using Anomalous Diffraction.
Authors: Pompidor, G. / Maury, O. / Vicat, J. / Kahn, R.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Gd-Hpdo3A, a Complex to Obtain High-Phasing-Power Heavy-Atom Derivatives for Sad and MAD Experiments: Results with Tetragonal Hen Egg-White Lysozyme.
Authors: Girard, E. / Chantalat, L. / Vicat, J. / Kahn, R.
History
DepositionSep 14, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references
Revision 1.2Mar 25, 2015Group: Database references
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.pdbx_ptnr2_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

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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)15,88116
Polymers14,3311
Non-polymers1,55015
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.509, 77.509, 38.482
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-2006-

HOH

21A-2026-

HOH

31A-2065-

HOH

41A-2088-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein LYSOZYME C / 1 / 4-BETA-N-ACETYLMURAMIDASE C / ALLERGEN GAL D IV / GAL D 4 / HEWL / MURAMIDASE / MUCOPEPTIDE N- ...1 / 4-BETA-N-ACETYLMURAMIDASE C / ALLERGEN GAL D IV / GAL D 4 / HEWL / MURAMIDASE / MUCOPEPTIDE N-ACETYLMURAMOYL-HYDROLASE


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: ROCHE APPLIED SCIENCE POWDER, CATALOG NUMBER 10837059001
Source: (natural) GALLUS GALLUS (chicken) / Organ: EGG / References: UniProt: P00698, lysozyme

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Non-polymers , 6 types, 161 molecules

#2: Chemical ChemComp-DCJ / N-((1-(2,6-DICARBOXYPYRIDIN-4-YL)-1H-1,2,3-TRIAZOL-4-YL)METHYL)-2-HYDROXY-N,N-DIMETHYLETHANAMINIUM / HYDROXYETHYLCHOLINETRIAZOLEDIPICOLINATE


Mass: 336.323 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H18N5O5
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-EU3 / EUROPIUM (III) ION


Mass: 151.964 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Eu
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.68 Å3/Da / Density % sol: 27 % / Description: NONE
Crystal growTemperature: 293 K / pH: 4.6
Details: 0.1 M SODIUM ACETATE PH 4.6, 0.4-1.5 M SODIUM CHLORIDE, 0.00067 M PROTEIN, 0.012 M LANTHANIDE COMPLEX, 293 K, 3-7 DAYS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2010 / Details: MIRRORS
RadiationMonochromator: EITHER 111 OR 311 SILICON SINGLE CRISTALS / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.21→38.75 Å / Num. obs: 36469 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 7.6 % / Biso Wilson estimate: 10.84 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.8
Reflection shellResolution: 1.21→1.27 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.3 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSJANUARY 30 2009data reduction
SCALA3.3.16data scaling
SHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.207→38.755 Å / SU ML: 0.23 / σ(F): 1.35 / Phase error: 14.46 / Stereochemistry target values: ML
Details: ACCORDING TO THE HIGH RESOLUTION, ANISOTROPIC ADP REFINEMENT WAS APPLIED FOR ALL ATOMS LIGAND OCCUPANCIES WERE FIXED ACCORDING TO THE LANTHANIDE ION OCCUPANCIES
RfactorNum. reflection% reflection
Rfree0.1783 1823 5 %
Rwork0.1581 --
obs0.1591 36424 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.756 Å2 / ksol: 0.384 e/Å3
Displacement parametersBiso mean: 13.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.073 Å20 Å20 Å2
2--0.073 Å20 Å2
3----0.1459 Å2
Refinement stepCycle: LAST / Resolution: 1.207→38.755 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 87 146 1233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081236
X-RAY DIFFRACTIONf_angle_d1.2521689
X-RAY DIFFRACTIONf_dihedral_angle_d25.572526
X-RAY DIFFRACTIONf_chiral_restr0.088161
X-RAY DIFFRACTIONf_plane_restr0.005221
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2071-1.23970.27491360.23422576X-RAY DIFFRACTION98
1.2397-1.27620.19221380.21152627X-RAY DIFFRACTION100
1.2762-1.31740.20591380.18672620X-RAY DIFFRACTION100
1.3174-1.36450.20691380.17842625X-RAY DIFFRACTION100
1.3645-1.41910.21381390.16112649X-RAY DIFFRACTION100
1.4191-1.48370.15961380.14642629X-RAY DIFFRACTION100
1.4837-1.5620.16251400.13672646X-RAY DIFFRACTION100
1.562-1.65980.15451410.13492666X-RAY DIFFRACTION100
1.6598-1.7880.18821390.13292660X-RAY DIFFRACTION100
1.788-1.96790.18711410.14052674X-RAY DIFFRACTION100
1.9679-2.25260.16421430.14382698X-RAY DIFFRACTION100
2.2526-2.8380.18161420.15512724X-RAY DIFFRACTION100
2.838-38.77450.16921500.17072807X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.63420.55550.62151.3426-0.06841.2629-0.0664-0.05030.1402-0.0859-0.00280.0487-0.1016-0.05320.06810.0640.0062-0.01180.04920.00350.059319.99735.35624.8874
22.0029-0.0734-0.55813.43250.64181.9682-0.0438-0.2322-0.11880.2482-0.02280.01730.09310.14450.05850.0788-0.0079-0.01040.0980.020.06815.5023-7.461217.8975
33.21220.2297-0.46420.98260.14441.81720.0212-0.1863-0.0084-0.0082-0.013-0.00960.01140.0755-0.01250.0797-0.0054-0.00770.04470.00780.066123.78192.870610.9551
43.6428-3.31882.24847.5336-3.21712.9304-0.06280.22030.474-0.16010.053-0.0064-0.366-0.0323-0.02090.21480.01750.02730.1150.06160.177923.447212.0806-4.1369
50.24640.62880.51991.9290.83341.8424-0.0450.15020.0952-0.12560.04140.11790.0125-0.0238-0.0240.14650.001-0.01250.1924-0.00880.089321.09191.6918-8.9968
60.00020.00020.00030.00010.00020.0004-0.17821.70890.97130.0727-1.08822.20930.2081-1.57151.27860.2102-0.0388-0.01360.20720.00940.295921.9949-2.869915.7086
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:43)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 44:82)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 83:122)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 123:129)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 1133)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 1130:1132)

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