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

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Entry
Database: PDB / ID: 4bad
TitleHen egg-white lysozyme structure in complex with the europium tris- hydroxymethyltriazoledipicolinate complex at 1.35 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 / EUROPIUM (III) ION / Chem-HM6 / Lysozyme C
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 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. / 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 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LYSOZYME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,01016
Polymers14,3311
Non-polymers1,67815
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.403, 77.403, 38.473
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-2027-

HOH

21A-2068-

HOH

31A-2100-

HOH

41A-2148-

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, 174 molecules

#2: Chemical
ChemComp-HM6 / 4-(4-(hydroxymethyl)-1h-1,2,3-triazol-1-yl)pyridine-2,6-dicarboxylic acid / HYDROXYMETHYLTRIAZOLE DIPICOLINIC ACID


Mass: 264.194 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H8N4O5
#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.: 6 / 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.: 2 / Source method: obtained synthetically / Formula: Eu
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE SEQUENCE PROVIDED CORRESPOND TO THE RESIDUES 19 TO 147, I.E WITHOUT THE DELETED SIGNAL PEPTIDE

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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, 0.00025 M PROTEIN, 0.0027 M LANTHANIDE COMPLEX, 293 K, 3-7 DAYS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.886
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 27, 2009 / Details: KIRKPATRICK-BAEZ BI-MORPH MIRRORS
RadiationMonochromator: CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.886 Å / Relative weight: 1
ReflectionResolution: 1.35→19.24 Å / Num. obs: 26192 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 7.5 % / Biso Wilson estimate: 11.16 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.8
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.8 / % possible all: 99.2

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Processing

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

Resolution: 1.35→18.773 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 13.78 / Stereochemistry target values: ML
Details: ACCORDING TO THE HIGH RESOLUTION, ANISOTROPIC ADP REFINEMENT WAS APPLIED FOR ALL ATOMS. LIGANDS OCCUPANCIES WERE FIXED ACCORDING TO THE LANTHANIDE ION OCCUPANCY
RfactorNum. reflection% reflection
Rfree0.1719 1329 5.1 %
Rwork0.1517 --
obs0.1527 26140 99.59 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.447 Å2 / ksol: 0.382 e/Å3
Displacement parametersBiso mean: 13.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.2538 Å20 Å20 Å2
2---0.2538 Å20 Å2
3---0.5076 Å2
Refinement stepCycle: LAST / Resolution: 1.35→18.773 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 90 159 1249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191210
X-RAY DIFFRACTIONf_angle_d1.8151649
X-RAY DIFFRACTIONf_dihedral_angle_d29.458492
X-RAY DIFFRACTIONf_chiral_restr0.114160
X-RAY DIFFRACTIONf_plane_restr0.009221
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3499-1.40390.20391390.18922685X-RAY DIFFRACTION99
1.4039-1.46780.19751620.16172701X-RAY DIFFRACTION100
1.4678-1.54520.16381590.14672714X-RAY DIFFRACTION100
1.5452-1.64190.18721480.13872713X-RAY DIFFRACTION100
1.6419-1.76860.16671320.14092755X-RAY DIFFRACTION100
1.7686-1.94640.1811550.13792751X-RAY DIFFRACTION100
1.9464-2.22770.1631520.14122766X-RAY DIFFRACTION100
2.2277-2.80510.14691410.14852820X-RAY DIFFRACTION100
2.8051-18.77480.18081410.16272906X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 37.7944 Å / Origin y: 18.6379 Å / Origin z: 9.7564 Å
111213212223313233
T0.029 Å20.0017 Å20.0046 Å2-0.0488 Å2-0.0195 Å2--0.0451 Å2
L1.0043 °20.2291 °20.1876 °2-1.6716 °2-0.0086 °2--1.1052 °2
S-0.0141 Å °-0.0248 Å °0.0252 Å °-0.0559 Å °-0.0181 Å °0.0296 Å °-0.0174 Å °-0.0307 Å °0.0168 Å °
Refinement TLS groupSelection details: ALL

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