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- PDB-5l3h: Re-refinement of 4dd4; cisplatin coordination chemistry determina... -

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Basic information

Entry
Database: PDB / ID: 5l3h
TitleRe-refinement of 4dd4; cisplatin coordination chemistry determination at hen egg white lysozyme His15 with standard uncertainties
ComponentsLysozyme C
KeywordsHYDROLASE / 4dd4 re-refinement / platinum coordination geometries / histidine in hen egg white lysozyme / platinum ligand distances and angles standard uncertainties
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
AMMONIA / : / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHelliwell, J.R. / Tanley, S.W.M.
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: 4dd4
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 1.3Nov 29, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.4Aug 8, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 1.5Jan 10, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_id_ISSN ..._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

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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)15,70718
Polymers14,3311
Non-polymers1,37617
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-171 kcal/mol
Surface area6290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.832, 78.832, 37.021
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-341-

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, 94 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#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-NH3 / AMMONIA / Ammonia


Mass: 17.031 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NH3
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.01 Å3/Da / Density % sol: 38.7 %
Crystal growTemperature: 295 K / Method: batch mode / pH: 4.7
Details: CRYSTALLIZATION CONDITIONS: 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 MEDIA, 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: Feb 17, 2011 / Details: INCOATEC HELIOS CONFOCAL OPTICS
RadiationMonochromator: CONFOCAL MIRROR OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→24.93 Å / Num. obs: 11826 / % possible obs: 88.59 % / Redundancy: 14.6 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 22.2
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 5.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4dd4

4dd4
PDB Unreleased entry


Resolution: 1.7→24.929 Å / SU ML: 0.19 / SU R Cruickshank DPI: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.24
RfactorNum. reflection% reflection
Rfree0.2476 582 4.92 %
Rwork0.202 --
obs0.2041 11824 88.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 12.6 Å2
Refinement stepCycle: LAST / Resolution: 1.7→24.929 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 20 77 1098
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051091
X-RAY DIFFRACTIONf_angle_d0.7191463
X-RAY DIFFRACTIONf_dihedral_angle_d12.871394
X-RAY DIFFRACTIONf_chiral_restr0.026149
X-RAY DIFFRACTIONf_plane_restr0.002196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.8710.25781630.21213099X-RAY DIFFRACTION100
1.871-2.14170.23961690.22143098X-RAY DIFFRACTION100
2.1417-2.69780.21981160.19642291X-RAY DIFFRACTION72
2.6978-24.93150.26551340.19212754X-RAY DIFFRACTION83

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