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- PDB-6f2j: Crystal structure of Hen Egg-White Lysozyme co-crystallized in pr... -

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Basic information

Entry
Database: PDB / ID: 6f2j
TitleCrystal structure of Hen Egg-White Lysozyme co-crystallized in presence of 100 mM Tb-Xo4 and 100 mM sodium sulfate
ComponentsLysozyme C
KeywordsHYDROLASE / Tb-Xo4 / nucleation / phasing / crystallophore
Function / homology
Function and homology information


Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / 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
Tb-Xo4 / TERBIUM(III) ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsEngilberge, S. / Riobe, F. / Di Pietro, S. / Girard, E. / Dumont, E. / Maury, O.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-13-BS07-0007-01 France
CitationJournal: Chemistry / Year: 2018
Title: Unveiling the Binding Modes of the Crystallophore, a Terbium-based Nucleating and Phasing Molecular Agent for Protein Crystallography.
Authors: Engilberge, S. / Riobe, F. / Wagner, T. / Di Pietro, S. / Breyton, C. / Franzetti, B. / Shima, S. / Girard, E. / Dumont, E. / Maury, O.
History
DepositionNov 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Jan 17, 2024Group: 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
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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_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_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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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)15,6977
Polymers14,3311
Non-polymers1,3666
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint-44 kcal/mol
Surface area6860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.915, 77.915, 37.738
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-439-

HOH

21A-497-

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


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme

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Non-polymers , 5 types, 221 molecules

#2: Chemical ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Tb
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-7MT / Tb-Xo4


Mass: 556.353 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H23N5O4Tb
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 38.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM Sodium acetate pH 4.6, 200mM to 800 mM sodium chloride and 100 mM sodium sulfate. Tb-Xo4 was directly mixed with the protein solution at a final concentration of 100 mM prior to crystallization.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.3→38.96 Å / Num. obs: 29089 / % possible obs: 99.82 % / Redundancy: 14 % / Biso Wilson estimate: 13.34 Å2 / Rpim(I) all: 0.023 / Net I/σ(I): 22.3
Reflection shellResolution: 1.3→1.37 Å / Rpim(I) all: 0.253

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H87

1h87


Resolution: 1.3→34.84 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.96 / SU R Cruickshank DPI: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.054 / SU Rfree Blow DPI: 0.054 / SU Rfree Cruickshank DPI: 0.049
RfactorNum. reflection% reflectionSelection details
Rfree0.179 1450 5 %RANDOM
Rwork0.159 ---
obs0.16 28998 99.5 %-
Displacement parametersBiso mean: 16.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.8059 Å20 Å20 Å2
2--0.8059 Å20 Å2
3----1.6117 Å2
Refine analyzeLuzzati coordinate error obs: 0.14 Å
Refinement stepCycle: 1 / Resolution: 1.3→34.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 64 215 1280
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012144HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.053841HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d447SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes29HARMONIC2
X-RAY DIFFRACTIONt_gen_planes325HARMONIC5
X-RAY DIFFRACTIONt_it2144HARMONIC20
X-RAY DIFFRACTIONt_nbd8SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.74
X-RAY DIFFRACTIONt_other_torsion12.61
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion136SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2617SEMIHARMONIC4
LS refinement shellResolution: 1.3→1.35 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.213 135 5.01 %
Rwork0.1961 2561 -
all0.197 2696 -
obs--96.29 %
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)
10.4750.50870.2820.7630.34630.44070.04360.10190-0.0441-0.05050.16690.055-0.0070.00680.052-0.0012-0.03310.0877-0.02680.1009-6.962715.51599.6944
20.2383-0.04370.15120.3485-0.17610.45610.01310.031-0.04970.03520.0990.092-0.0328-0.0459-0.1120.0405-0.00840.03350.0756-0.04080.1235-11.773523.422520.6898
30.5216-0.04160.33210.75740.07651.07230.04490.066-0.04080.0047-0.04920.0161-0.03820.03190.00430.02160.0087-0.01030.0494-0.0090.0576-0.054121.328612.7268
40.2520.0513-0.02810.00040.08570.0011-0.02390.0954-0.03980.1238-0.0203-0.0701-0.0981-0.01310.04420.08050.0054-0.04320.0998-0.00860.106814.036919.455323.135
51.01310.3079-0.77050.5730.03540.6558-0.0612-0.0419-0.070.10020.0028-0.0573-0.0311-0.05580.05840.06620.0322-0.01840.0609-0.00360.06356.721516.489825.8586
60.6715-0.30070.06451.2357-0.84910.2142-0.0702-0.1327-0.1580.08260.03760.1001-0.0047-0.02760.03260.06840.02480.01110.0808-0.00380.08662.764111.591126.4466
70.3794-0.72060.27790.4132-0.25460.5914-0.04740.0105-0.08480.11830.05990.0547-0.0143-0.0319-0.01250.06610.01860.01790.0595-0.00590.0674-3.876521.987325.1568
80.06390.3636-0.21440.0920.237200.0191-0.0635-0.01040.0204-0.0613-0.0433-0.09460.08090.04220.0542-0.0126-0.00970.10360.02930.08662.721931.315517.5061
90.20420.2780.09670.00390.53170.97290.0063-0.0430.0133-0.1523-0.06720.0722-0.1521-0.13320.06090.07590.0334-0.04180.0710.00620.0709-8.921327.96037.7555
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1 - A|14 }
2X-RAY DIFFRACTION2{ A|15 - A|24 }
3X-RAY DIFFRACTION3{ A|25 - A|42 }
4X-RAY DIFFRACTION4{ A|43 - A|50 }
5X-RAY DIFFRACTION5{ A|51 - A|68 }
6X-RAY DIFFRACTION6{ A|69 - A|88 }
7X-RAY DIFFRACTION7{ A|89 - A|108 }
8X-RAY DIFFRACTION8{ A|109 - A|114 }
9X-RAY DIFFRACTION9{ A|115 - A|129 }

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