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- PDB-4lt2: HEWL co-crystallized with Carboplatin in non-NaCl conditions: cry... -

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Basic information

Entry
Database: PDB / ID: 4lt2
TitleHEWL co-crystallized with Carboplatin in non-NaCl conditions: crystal 2 processed using the EVAL 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: To be Published
Title: Carboplatin binding to a model protein in non-NaCl conditions to eliminate partial conversion to cisplatin, and the use of different criteria to choose the resolution limit
Authors: Tanley, S.W.M. / Diederichs, K. / Kroon-Batenburg, L.M.J. / Schreurs, A.M.M. / Helliwell, J.R.
History
DepositionJul 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.3Sep 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 1.4Nov 27, 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)15,5829
Polymers14,3311
Non-polymers1,2518
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.294, 77.294, 36.628
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-336-

HOH

21A-342-

HOH

31A-364-

HOH

41A-367-

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-QPT / carboplatin


Mass: 371.248 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12N2O4Pt / Comment: medication, chemotherapy*YM
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 1.91 Å3/Da / Density % sol: 35.56 %
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→25.15 Å / Num. all: 7901 / Num. obs: 7501 / % possible obs: 94.9 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 1.1 / Redundancy: 21.6 % / Rmerge(I) obs: 0.193 / Net I/σ(I): 14.2
Reflection shellResolution: 2→2.04 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.41 / Mean I/σ(I) obs: 1.1 / % possible all: 93.7

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Processing

Software
NameVersionClassification
APEXdata collection
PHASERphasing
REFMAC5.7.0032refinement
EVAL15data reduction
EVAL15data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W1Y

2w1y


Resolution: 2→25.15 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.887 / SU B: 5.932 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 1.1 / ESU R: 0.254 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26507 369 4.7 %RANDOM
Rwork0.20771 ---
obs0.21041 7501 99.22 %-
all-7901 --
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: 22.839 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å2-0 Å2-0 Å2
2---0.79 Å2-0 Å2
3---1.58 Å2
Refinement stepCycle: LAST / Resolution: 2→25.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 35 70 1106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191052
X-RAY DIFFRACTIONr_bond_other_d0.0010.02993
X-RAY DIFFRACTIONr_angle_refined_deg1.8151.9251417
X-RAY DIFFRACTIONr_angle_other_deg0.953.0072238
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1415128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9722350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.39815166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.1011511
X-RAY DIFFRACTIONr_chiral_restr0.1060.2151
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021208
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02273
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_it1.5721.933515
X-RAY DIFFRACTIONr_mcbond_other1.5521.927514
X-RAY DIFFRACTIONr_mcangle_it2.4042.885642
X-RAY DIFFRACTIONr_mcangle_other2.4062.891643
X-RAY DIFFRACTIONr_scbond_it2.9482.397535
X-RAY DIFFRACTIONr_scbond_other2.9452.394534
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8053.42775
X-RAY DIFFRACTIONr_long_range_B_refined6.17116.61281
X-RAY DIFFRACTIONr_long_range_B_other6.1716.6231282
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
Rfree0.313 32 -
Rwork0.224 516 -
obs--94.65 %

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