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- PDB-4lt0: HEWL co-crystallized with Carboplatin in non-NaCl conditions: cry... -

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Basic information

Entry
Database: PDB / ID: 4lt0
TitleHEWL co-crystallized with Carboplatin in non-NaCl conditions: crystal 1 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


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
carboplatin / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.5Sep 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

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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)15,2518
Polymers14,3311
Non-polymers9207
Water75742
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.745, 76.745, 36.315
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-332-

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-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


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


Mass: 371.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12N2O4Pt / Comment: medication, chemotherapy*YM
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 1.87 Å3/Da / Density % sol: 34.07 %
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 1 week after crystal growth, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Mar 22, 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→19.19 Å / Num. all: 7770 / Num. obs: 6342 / % possible obs: 81.6 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 0.9 / Redundancy: 26.1 % / Rmerge(I) obs: 0.34 / Net I/σ(I): 9.2
Reflection shellResolution: 2→2.03 Å / Redundancy: 12.3 % / Rmerge(I) obs: 2.71 / Mean I/σ(I) obs: 0.9 / % possible all: 99.8

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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: 2.1→19.19 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.894 / SU B: 12.387 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(F): 4 / ESU R: 0.349 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28274 315 4.7 %RANDOM
Rwork0.22298 ---
all0.226 7770 --
obs0.22577 6342 98.9 %-
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: 26.844 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å2-0 Å2-0 Å2
2---1.05 Å2-0 Å2
3---2.1 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 37 42 1080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191055
X-RAY DIFFRACTIONr_bond_other_d0.0020.02998
X-RAY DIFFRACTIONr_angle_refined_deg1.8881.931424
X-RAY DIFFRACTIONr_angle_other_deg0.9453.0072250
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8625128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.2112350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98315166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.651511
X-RAY DIFFRACTIONr_chiral_restr0.0990.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021206
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02271
X-RAY DIFFRACTIONr_mcbond_it1.3751.666515
X-RAY DIFFRACTIONr_mcbond_other1.3661.663514
X-RAY DIFFRACTIONr_mcangle_it2.1422.489641
X-RAY DIFFRACTIONr_mcangle_other2.1422.492642
X-RAY DIFFRACTIONr_scbond_it2.5132.11537
X-RAY DIFFRACTIONr_scbond_other2.5112.115538
X-RAY DIFFRACTIONr_scangle_other3.6513.018781
X-RAY DIFFRACTIONr_long_range_B_refined6.47614.3251302
X-RAY DIFFRACTIONr_long_range_B_other6.47414.3511303
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 24 -
Rwork0.238 454 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -19.6533 Å / Origin y: -1.4986 Å / Origin z: -8.6632 Å
111213212223313233
T0.0725 Å2-0.007 Å2-0.0147 Å2-0.0783 Å2-0.0118 Å2--0.0479 Å2
L0.7131 °20.5992 °20.2512 °2-1.0249 °20.0982 °2--0.5857 °2
S0.0706 Å °-0.0081 Å °-0.0941 Å °0.01 Å °-0.0469 Å °0.0329 Å °-0.0961 Å °0.0664 Å °-0.0237 Å °

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