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- PDB-4nsh: Carboplatin binding to HEWL in 0.2M NH4SO4, 0.1M NaAc in 25% PEG ... -

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Basic information

Entry
Database: PDB / ID: 4nsh
TitleCarboplatin binding to HEWL in 0.2M NH4SO4, 0.1M NaAc in 25% PEG 4000 at pH 4.6
ComponentsLysozyme C
KeywordsHYDROLASE
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
ACETATE ION / 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. / Levy, C. / Schreurs, A.M.M. / Helliwell, J.R.
CitationJournal: Acta Crystallogr F Struct Biol Commun / 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
DepositionNov 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.source
Revision 1.2Sep 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 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)15,58110
Polymers14,3311
Non-polymers1,2509
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.085, 77.085, 37.143
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-208-

SO4

21A-316-

HOH

31A-357-

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) / References: UniProt: P00698, lysozyme

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Non-polymers , 5 types, 74 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-QPT / carboplatin


Mass: 371.248 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12N2O4Pt / Comment: medication, chemotherapy*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 1.93 Å3/Da / Density % sol: 36.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 20mg of HEWL (0.6mM) was dissolved in 1ml distilled water. 1.4mg of carboplatin (1.8mM) was added with 75 l DMSO. 2 l of this mixed with 2 l resevoir soultion 0.2M NH4SO4, 0.1M NaAc in 25% ...Details: 20mg of HEWL (0.6mM) was dissolved in 1ml distilled water. 1.4mg of carboplatin (1.8mM) was added with 75 l DMSO. 2 l of this mixed with 2 l resevoir soultion 0.2M NH4SO4, 0.1M NaAc in 25% PEG 4000 at pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Jul 29, 2013
RadiationMonochromator: confocal mirror optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→30.71 Å / Num. all: 6965 / Num. obs: 6593 / % possible obs: 94.6 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 20.8 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 19.2
Reflection shellResolution: 2.1→2.13 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 2.2 / % possible all: 99.7

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Processing

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

2w1y


Resolution: 2.1→30.71 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.905 / SU B: 11.476 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2 / ESU R: 0.301 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26188 327 4.7 %RANDOM
Rwork0.19627 ---
all0.199 6965 --
obs0.19934 6593 99.65 %-
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: 21.758 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å2-0 Å2-0 Å2
2---0.56 Å2-0 Å2
3---1.13 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 38 65 1104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191054
X-RAY DIFFRACTIONr_bond_other_d00.02979
X-RAY DIFFRACTIONr_angle_refined_deg1.1511.9261419
X-RAY DIFFRACTIONr_angle_other_deg0.6293.0072208
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0245128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.132350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62915166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3351511
X-RAY DIFFRACTIONr_chiral_restr0.0640.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021222
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02275
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_it0.8931.579518
X-RAY DIFFRACTIONr_mcbond_other0.8841.563514
X-RAY DIFFRACTIONr_mcangle_it1.5392.343642
X-RAY DIFFRACTIONr_mcangle_other1.5392.348643
X-RAY DIFFRACTIONr_scbond_it1.0971.832534
X-RAY DIFFRACTIONr_scbond_other1.0971.837535
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8362.664775
X-RAY DIFFRACTIONr_long_range_B_refined4.25513.571300
X-RAY DIFFRACTIONr_long_range_B_other4.25413.5851301
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.099→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 23 -
Rwork0.21 471 -
obs--99.8 %
Refinement TLS params.Method: refined / Origin x: -19.6644 Å / Origin y: -1.4718 Å / Origin z: -8.7971 Å
111213212223313233
T0.0348 Å2-0.0142 Å2-0.0012 Å2-0.0173 Å2-0.0077 Å2--0.0554 Å2
L0.4805 °20.5265 °20.0916 °2-0.7386 °20.0151 °2--0.6876 °2
S0.0011 Å °-0.0137 Å °-0.0972 Å °0.0032 Å °-0.0317 Å °-0.0448 Å °-0.0711 Å °0.0084 Å °0.0305 Å °

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