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- PDB-4yeo: Triclinic HEWL co-crystallised with cisplatin, studied at a data ... -

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Basic information

Entry
Database: PDB / ID: 4yeo
TitleTriclinic HEWL co-crystallised with cisplatin, studied at a data collection temperature of 150K - new refinement
ComponentsLysozyme C
KeywordsHYDROLASE / Re-refinement of 4mwk / lysozyme / metal binding
Function / homology
Function and homology information


Lactose synthesis / 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 ...Lactose synthesis / 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
ACETATE ION / Cisplatin / NITRATE ION / : / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 0.98 Å
AuthorsShabalin, I.G. / Dauter, Z. / Jaskolski, M. / Minor, W. / Wlodawer, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin.
Authors: Shabalin, I. / Dauter, Z. / Jaskolski, M. / Minor, W. / Wlodawer, A.
#1: Journal: Struct Dyn / Year: 2014
Title: Structural dynamics of cisplatin binding to histidine in a protein.
Authors: Tanley, S.W. / Helliwell, J.R.
History
DepositionFeb 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Data collection
Revision 1.2Sep 9, 2015Group: Database references
Revision 1.3Sep 16, 2015Group: Database references
Revision 1.4Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.6Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.8Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)16,08117
Polymers14,2891
Non-polymers1,79216
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)26.998, 31.807, 34.072
Angle α, β, γ (deg.)89.080, 72.000, 67.810
Int Tables number1
Space group name H-MP1

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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: 14289.080 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 , 7 types, 232 molecules

#2: Chemical ChemComp-CPT / Cisplatin / diammine(dichloro)platinum / Cisplatin


Mass: 300.045 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl2H6N2Pt / Comment: medication, chemotherapy*YM
#3: Chemical
ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Pt
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: NO3
#7: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 1.89 Å3/Da / Density % sol: 31.34 %
Crystal growTemperature: 294 K / Method: evaporation / pH: 4.7
Details: 40mg HEWL co-crystallised with 2.6mg cisplatin, with the platinum compounds being in a 3-fold molar excess to the protein. 462.5 ul of a 0.02M NaAc solution along with 462.5 ul of a 0.5M ...Details: 40mg HEWL co-crystallised with 2.6mg cisplatin, with the platinum compounds being in a 3-fold molar excess to the protein. 462.5 ul of a 0.02M NaAc solution along with 462.5 ul of a 0.5M NaNo3 solution was used with 75 ul DMSO added

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Dec 7, 2012
RadiationMonochromator: CONFOCAL MIRROR OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 0.98→29.28 Å / Num. obs: 48959 / % possible obs: 94.8 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 6 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 15.6
Reflection shellResolution: 0.98→1.02 Å / Redundancy: 0.6 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 3.2 / % possible all: 51.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
SAINTdata reduction
APEXdata scaling
PHASERphasing
Cootmodel building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4mwk

4mwk
PDB Unreleased entry


Resolution: 0.98→29.26 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.977 / WRfactor Rfree: 0.139 / WRfactor Rwork: 0.119 / FOM work R set: 0.9356 / SU B: 0.558 / SU ML: 0.014 / SU R Cruickshank DPI: 0.0219 / SU Rfree: 0.0223 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.022 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY This deposit resulted from an analysis of a number of PDB entries that contain cisplatin or carboplatin in ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY This deposit resulted from an analysis of a number of PDB entries that contain cisplatin or carboplatin in complex with proteins, conducted in the spirit of the Terwilliger-Bricogne motto advocating continuous improvement of the macromolecular models in the PDB (Acta Cryst. D70, 2533, 2014). The structure factors and coordinates, originally deposited as 4mwk, were used as the starting point for an independent re-refinement. The new model includes some reinterpretation of the ligands, has lower R factors, and improved statistics describing the agreement with the experimental data.
RfactorNum. reflection% reflectionSelection details
Rfree0.1313 2646 5.1 %RANDOM
Rwork0.1123 ---
obs0.1133 48959 90.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 48.05 Å2 / Biso mean: 7.982 Å2 / Biso min: 2.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.02 Å20.12 Å2
2--0.09 Å20 Å2
3----0.08 Å2
Refinement stepCycle: final / Resolution: 0.98→29.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms997 0 55 233 1285
Biso mean--10.3 17.93 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191116
X-RAY DIFFRACTIONr_bond_other_d0.0020.021022
X-RAY DIFFRACTIONr_angle_refined_deg1.7111.9231506
X-RAY DIFFRACTIONr_angle_other_deg1.35832334
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6275143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.99823.33354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.70715180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7671511
X-RAY DIFFRACTIONr_chiral_restr0.1030.2155
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021321
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02290
X-RAY DIFFRACTIONr_mcbond_it0.6950.562537
X-RAY DIFFRACTIONr_mcbond_other0.69444.403535
X-RAY DIFFRACTIONr_mcangle_it0.9480.845672
X-RAY DIFFRACTIONr_rigid_bond_restr5.39631116
X-RAY DIFFRACTIONr_sphericity_free11.1650.126
X-RAY DIFFRACTIONr_sphericity_bonded6.3160.11270
LS refinement shellResolution: 0.98→1.005 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.194 90 -
Rwork0.177 2029 -
all-2119 -
obs--49.71 %

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