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- PDB-5l3i: Re-refinement of 4dd6; cisplatin coordination chemistry determina... -

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Basic information

Entry
Database: PDB / ID: 5l3i
TitleRe-refinement of 4dd6; cisplatin coordination chemistry determination at hen egg white lysozyme His15
ComponentsLysozyme C
KeywordsHYDROLASE / 4dd6 re-refinements / platinum coordination geometries / histidine / hen egg white 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
AMMONIA / : / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHelliwell, J.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council United Kingdom
Citation
Journal: ArXiv / Year: 2016
Title: Cisplatin coordination chemistry determination at hen egg white lysozyme His15 with ligand distances and angles, and their standard uncertainties, and also reporting a split occupancy effect
Authors: Helliwell, J.R. / Schreurs, A.M.M. / Kroon-Batenburg, L.M.J. / Tanley, S.
#1: Journal: ArXiv / Year: 2016
Title: Cisplatin coordination chemistry determination at hen egg white lysozyme His15 with ligand distances and angles, and their standard uncertainties, and also reporting a split occupancy effect
Authors: Helliwell, J.R. / Tanley, S. / Schreurs, A.M.M. / Kroon-Batenburg, L.M.J.
History
DepositionMay 6, 2016Deposition site: PDBE / Processing site: PDBE
SupersessionJun 15, 2016ID: 4dd6
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn
Item: _atom_site.occupancy / _citation.country ..._atom_site.occupancy / _citation.country / _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 2.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)15,82819
Polymers14,3311
Non-polymers1,49718
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-159 kcal/mol
Surface area6240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.016, 78.016, 37.071
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-325-

HOH

21A-358-

HOH

31A-361-

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) / Plasmid details: hen egg white / References: UniProt: P00698, lysozyme

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Non-polymers , 6 types, 79 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Pt
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NH3 / AMMONIA


Mass: 17.031 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NH3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 1.97 Å3/Da / Density % sol: 37.5 %
Crystal growTemperature: 295 K / Method: batch mode / pH: 4.7
Details: HEWL CO-CRYSTALLIZED WITH CISPLATIN IN 462.5 microL 0.05 M SODIUM ACETATE AND 462.5 microL 10% SODIUM CHLORIDE IN 75 microL DMSO, PH 4.7, BATCH, TEMPERATURE 295K.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Nov 25, 2010 / Details: CONFOCAL MIRROR OPTICS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→18.39 Å / Num. obs: 10869 / % possible obs: 83.05 % / Redundancy: 25 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 35.1
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 18 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 8.1 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: 1.9_1692 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4dd6

4dd6
PDB Unreleased entry


Resolution: 1.7→18.389 Å / SU ML: 0.14 / SU R Cruickshank DPI: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.15
RfactorNum. reflection% reflection
Rfree0.2121 530 4.88 %
Rwork0.181 --
obs0.1825 10868 83.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→18.389 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 27 61 1089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071112
X-RAY DIFFRACTIONf_angle_d0.9841491
X-RAY DIFFRACTIONf_dihedral_angle_d12.085400
X-RAY DIFFRACTIONf_chiral_restr0.036152
X-RAY DIFFRACTIONf_plane_restr0.004199
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6997-1.87060.24091750.17953022X-RAY DIFFRACTION100
1.8706-2.14090.2088830.17231682X-RAY DIFFRACTION55
2.1409-2.69590.20191480.18283019X-RAY DIFFRACTION100
2.6959-18.38960.20941240.18252615X-RAY DIFFRACTION100

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