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- PDB-4lt3: HEWL co-crystallized with Carboplatin in non-NaCl conditions: cry... -

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Basic information

Entry
Database: PDB / ID: 4lt3
TitleHEWL co-crystallized with Carboplatin in non-NaCl conditions: crystal 2 processed using the XDS software package
ComponentsLysozyme C
KeywordsHYDROLASE / histidine / MPD / avoid partial conversion to cisplatin / pair-wise refinement technique / DPI / resolution limit choice / glycosyl hydrolase
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
carboplatin / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTanley, S.W.M. / Diederichs, K. / Kroon-Batenburg, L.M.J. / Schreurs, A.M.M. / Helliwell, J.R.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Carboplatin binding to histidine.
Authors: Tanley, S.W. / Diederichs, K. / Kroon-Batenburg, L.M. / Levy, C. / Schreurs, A.M. / Helliwell, J.R.
History
DepositionJul 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Sep 24, 2014Group: Database references
Revision 1.3Mar 7, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.source
Revision 1.4Sep 20, 2023Group: 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 / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 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)15,6239
Polymers14,3311
Non-polymers1,2918
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.120, 77.120, 36.560
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-327-

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 / Fragment: UNP residues 19-147 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-QPT / carboplatin


Mass: 371.248 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12N2O4Pt / Comment: medication*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 1.9 Å3/Da / Density % sol: 35.15 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 2 uL protein/carboplatin/DMSO solution [20 mg (0.6 mM) HEWL + 1.4 mg (1.8 mM) carboplatin in 1 mL distilled water + 75 uL DMSO] + 2 uL reservoir solution [65% MPD, 0.1 M citric acid, pH 4.0] ...Details: 2 uL protein/carboplatin/DMSO solution [20 mg (0.6 mM) HEWL + 1.4 mg (1.8 mM) carboplatin in 1 mL distilled water + 75 uL DMSO] + 2 uL reservoir solution [65% MPD, 0.1 M citric acid, pH 4.0] against 1 mL of reservoir solution, crystals grew after ~4 weeks, data collected 5 weeks after crystal growth, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 127 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: APEX II CCD / Detector: CCD / Date: May 8, 2013
RadiationMonochromator: tunable graphite crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→39.41 Å / Num. all: 7850 / Num. obs: 7488 / % possible obs: 95 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 0.5 / Rmerge(I) obs: 0.248 / Net I/σ(I): 14.6
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 2.27 / Mean I/σ(I) obs: 0.5 / % possible all: 32.4

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Processing

Software
NameVersionClassification
APEXdata collection
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W1Y

2w1y


Resolution: 2→27.28 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.903 / SU B: 5.823 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 4 / ESU R: 0.234 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2575 362 4.6 %RANDOM
Rwork0.19574 ---
obs0.19865 7488 99.61 %-
all-7850 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.677 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0 Å2-0 Å2
2---0.49 Å2-0 Å2
3---0.98 Å2
Refinement stepCycle: LAST / Resolution: 2→27.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 41 44 1086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191058
X-RAY DIFFRACTIONr_bond_other_d0.0010.02998
X-RAY DIFFRACTIONr_angle_refined_deg1.651.9321426
X-RAY DIFFRACTIONr_angle_other_deg0.9333.0072250
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5925128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3572350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.72915166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8951511
X-RAY DIFFRACTIONr_chiral_restr0.0960.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021206
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02271
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_it1.8472.418515
X-RAY DIFFRACTIONr_mcbond_other1.8222.411514
X-RAY DIFFRACTIONr_mcangle_it2.8083.614642
X-RAY DIFFRACTIONr_mcangle_other2.813.621643
X-RAY DIFFRACTIONr_scbond_it3.1092.96542
X-RAY DIFFRACTIONr_scbond_other2.8272.911536
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3744.214780
X-RAY DIFFRACTIONr_long_range_B_refined6.88220.571265
X-RAY DIFFRACTIONr_long_range_B_other6.88420.5581264
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.565 18 -
Rwork0.314 532 -
obs--95.82 %

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