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- PDB-4ddb: EVAL processed HEWL, cisplatin DMSO paratone pH 6.5 -

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Basic information

Entry
Database: PDB / ID: 4ddb
TitleEVAL processed HEWL, cisplatin DMSO paratone pH 6.5
ComponentsLysozyme C
KeywordsHYDROLASE / hen egg white lysozyme (HEWL) / platinum / N-acetylglucosamine
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
Cisplatin / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsTanley, S.W. / Schreurs, A.M. / Kroon-Batenburg, L.M. / Meredith, J. / Prendergast, R. / Walsh, D. / Bryant, P. / Levy, C. / Helliwell, J.R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structural studies of the effect that dimethyl sulfoxide (DMSO) has on cisplatin and carboplatin binding to histidine in a protein.
Authors: Tanley, S.W. / Schreurs, A.M. / Kroon-Batenburg, L.M. / Meredith, J. / Prendergast, R. / Walsh, D. / Bryant, P. / Levy, C. / Helliwell, J.R.
History
DepositionJan 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 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 1.4Oct 16, 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)15,71313
Polymers14,3311
Non-polymers1,38112
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.641, 79.641, 37.018
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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) / Tissue: egg white / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-CPT / Cisplatin / diammine(dichloro)platinum


Mass: 300.045 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl2H6N2Pt / Comment: medication*YM
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.05 Å3/Da / Density % sol: 39.94 %
Crystal growTemperature: 277 K / Method: batch / pH: 6.5
Details: HEWL co-crystallized with cisplatin in 462.5 uL 0.05 M sodium acetate, pH 6.5, 462.5 uL 10% sodium chloride, and 75 uL DMSO, BATCH, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 9, 2011 / Details: Osmic Confocal Max-Flux, blue configuration
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: 2.5→30.94 Å / Num. all: 3234 / Num. obs: 1772 / % possible obs: 54.7 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 24.6 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 22.6
Reflection shellResolution: 2.5→2.58 Å / Redundancy: 24.5 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 6.1 / % possible all: 97.3

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERMRphasing
REFMAC5.6.0117refinement
EVAL1515data reduction
EVAL1515data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W1Y

2w1y


Resolution: 3→28.16 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.842 / SU B: 48.053 / SU ML: 0.499 / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2 / ESU R Free: 0.748 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2795 73 4 %RANDOM
Rwork0.21399 ---
obs0.21684 1772 70.1 %-
all-3234 --
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: 17.811 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--0.22 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 3→28.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 48 31 1080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191064
X-RAY DIFFRACTIONr_bond_other_d0.0020.02708
X-RAY DIFFRACTIONr_angle_refined_deg1.1731.9331428
X-RAY DIFFRACTIONr_angle_other_deg2.2233.0091685
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0015128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.7512350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.2715166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5991511
X-RAY DIFFRACTIONr_chiral_restr0.0640.2155
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021172
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02235
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 4 -
Rwork0.24 145 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -0.2933 Å / Origin y: -20.8895 Å / Origin z: 8.9398 Å
111213212223313233
T0.0885 Å2-0.0223 Å20.0025 Å2-0.074 Å2-0.0005 Å2--0.0231 Å2
L0.8169 °20.4015 °2-0.1394 °2-1.3471 °2-0.5546 °2--1.7655 °2
S0.0196 Å °-0.0058 Å °-0.0676 Å °-0.0515 Å °-0.0095 Å °0.0861 Å °-0.053 Å °-0.0213 Å °-0.0102 Å °

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