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- PDB-6g5y: The X-ray structure of the adduct formed in the reaction between ... -

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Basic information

Entry
Database: PDB / ID: 6g5y
TitleThe X-ray structure of the adduct formed in the reaction between lysozyme and a platinum(II) terpyridine compound (acid pH)
ComponentsLysozyme C
KeywordsHYDROLASE / Platinum terpyridine compounds / Protein metalation / ESI MS elucidation / X-Ray structure determination
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
NITRATE ION / : / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsMerlino, A. / Ferraro, G.
CitationJournal: Dalton Trans / Year: 2018
Title: A case of extensive protein platination: the reaction of lysozyme with a Pt(ii)-terpyridine complex.
Authors: Ferraro, G. / Marzo, T. / Infrasca, T. / Cilibrizzi, A. / Vilar, R. / Messori, L. / Merlino, A.
History
DepositionMar 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_symmetry

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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)16,62519
Polymers14,3311
Non-polymers2,29418
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-116 kcal/mol
Surface area6870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.490, 78.490, 36.730
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-326-

HOH

21A-366-

HOH

31A-418-

HOH

41A-420-

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-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#3: Chemical
ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Pt
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 1.97 Å3/Da / Density % sol: 37.68 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 20% ethylene glicol, 0.10 M sodium acetate pH 4.4, 0.60 M sodium nitrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.96771 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96771 Å / Relative weight: 1
ReflectionResolution: 1.49→55.51 Å / Num. obs: 18842 / % possible obs: 98.3 % / Redundancy: 3.7 % / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.025 / Net I/σ(I): 18.1
Reflection shellResolution: 1.49→1.57 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 3.1 / CC1/2: 0.672 / Rpim(I) all: 0.219 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→55.5 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.502 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.097 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24002 952 5.1 %RANDOM
Rwork0.19331 ---
obs0.19566 17866 97.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.439 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å20 Å20 Å2
2---1.06 Å20 Å2
3---2.12 Å2
Refinement stepCycle: 1 / Resolution: 1.49→55.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 48 121 1170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191145
X-RAY DIFFRACTIONr_bond_other_d0.0030.021016
X-RAY DIFFRACTIONr_angle_refined_deg2.0781.9521570
X-RAY DIFFRACTIONr_angle_other_deg1.20932337
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2895144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.33522.98257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34715181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5921513
X-RAY DIFFRACTIONr_chiral_restr0.1280.2159
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211357
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02265
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_it2.1122.391558
X-RAY DIFFRACTIONr_mcbond_other2.0962.386557
X-RAY DIFFRACTIONr_mcangle_it2.873.591708
X-RAY DIFFRACTIONr_mcangle_other2.8783.596709
X-RAY DIFFRACTIONr_scbond_it2.9622.768587
X-RAY DIFFRACTIONr_scbond_other2.962.77588
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6424.071885
X-RAY DIFFRACTIONr_long_range_B_refined6.12329.841411
X-RAY DIFFRACTIONr_long_range_B_other6.12229.8591412
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.492→1.531 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 79 -
Rwork0.369 1314 -
obs--99.79 %

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