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- PDB-4yem: Carboplatin binding to HEWL in NaBr crystallisation conditions st... -

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Basic information

Entry
Database: PDB / ID: 4yem
TitleCarboplatin binding to HEWL in NaBr crystallisation conditions studied at an X-ray wavelength of 0.9163A - new refinement
ComponentsLysozyme C
KeywordsHYDROLASE / Re-refinement of 4XAN / Carboplatin / Metal binding / lysozyme
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 / BROMIDE ION / : / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.47 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.
History
DepositionFeb 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Sep 16, 2015Group: Data collection
Revision 1.3Sep 30, 2015Group: Data collection
Revision 1.4Nov 4, 2015Group: Database references
Revision 1.5Sep 6, 2017Group: Author supporting evidence / Data collection / Derived calculations
Category: diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
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
Revision 1.9Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)16,46925
Polymers14,3311
Non-polymers2,13724
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.580, 78.580, 37.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-209-

BR

21A-334-

HOH

31A-363-

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 , 7 types, 204 molecules

#2: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Pt
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


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


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.01 Å3/Da / Density % sol: 38.76 %
Crystal growTemperature: 297 K / Method: batch mode / pH: 4.7
Details: co-crystallizing 20 mg ml HEWL with 1.4 mg carboplatin in 75 ml DMSO, 462.5 ml 0.1 M sodium acetate, 462.5 ml 1 M NaBr solution.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9163 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2013
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9163 Å / Relative weight: 1
ReflectionResolution: 1.47→55.56 Å / Num. all: 18627 / Num. obs: 17672 / % possible obs: 94.6 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 10.6 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 16.3
Reflection shellResolution: 1.47→1.5 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.2 / % possible all: 64

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
xia2data reduction
MOSFLMdata reduction
Aimlessdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4XAN

4xan
PDB Unreleased entry


Resolution: 1.47→39.29 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.1545 / WRfactor Rwork: 0.1032 / FOM work R set: 0.9142 / SU B: 2.228 / SU ML: 0.037 / SU R Cruickshank DPI: 0.0743 / SU Rfree: 0.0648 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.065 / 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 4xan (4nsf), 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
Rfree0.1559 933 5 %RANDOM
Rwork0.1053 ---
obs0.1077 17672 91.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.86 Å2 / Biso mean: 14.86 Å2 / Biso min: 6.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.2 Å2
Refinement stepCycle: final / Resolution: 1.47→39.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 36 182 1219
Biso mean--26.01 30.4 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191106
X-RAY DIFFRACTIONr_bond_other_d0.0020.021038
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.9121507
X-RAY DIFFRACTIONr_angle_other_deg1.92332367
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8465145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.30222.71259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.44415188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2931515
X-RAY DIFFRACTIONr_chiral_restr0.1130.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021319
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02302
X-RAY DIFFRACTIONr_mcbond_it1.2371.09534
X-RAY DIFFRACTIONr_mcbond_other1.188532
X-RAY DIFFRACTIONr_mcangle_it1.511.629669
X-RAY DIFFRACTIONr_rigid_bond_restr1.87131106
X-RAY DIFFRACTIONr_sphericity_free25.7290.0169
X-RAY DIFFRACTIONr_sphericity_bonded10.6090.011213
LS refinement shellResolution: 1.47→1.508 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.175 39 -
Rwork0.138 913 -
all-952 -
obs--64.11 %

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