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- PDB-4g49: Room temperature X-ray diffraction of cisplatin binding to HEWL i... -

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Basic information

Entry
Database: PDB / ID: 4g49
TitleRoom temperature X-ray diffraction of cisplatin binding to HEWL in aqueous media after 15 months of crystal storage
ComponentsLysozyme C
KeywordsHYDROLASE / cisplatin / carboplatin / aqueous media / DMSO media / omega scan data collection / capillaries
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
ACETATE ION / Cisplatin / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.4 Å
AuthorsTanley, S.W.M. / Schreurs, A.M.M. / Kroon-Batenburg, L.M.J. / Helliwell, J.R.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Room-temperature X-ray diffraction studies of cisplatin and carboplatin binding to His15 of HEWL after prolonged chemical exposure.
Authors: Tanley, S.W. / Schreurs, A.M. / Kroon-Batenburg, L.M. / Helliwell, J.R.
History
DepositionJul 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Sep 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 / pdbx_struct_conn_angle / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _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_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

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1207
Polymers14,3311
Non-polymers7896
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.671, 78.671, 38.068
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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CPT / Cisplatin / diammine(dichloro)platinum / Cisplatin


Mass: 300.045 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl2H6N2Pt / Comment: medication, chemotherapy*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.06 Å3/Da / Density % sol: 40.15 %
Crystal growTemperature: 295 K / Method: batch / pH: 4.7
Details: HEWL co-crystallized with cisplatin in 1 mL 10% sodium chloride + 1 ml 0.04 M sodium acetate, pH 4.7, BATCH, temperature 295K

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Jan 28, 2012
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: 2.4→55.629 Å / Num. all: 8952 / Num. obs: 4770 / % possible obs: 50 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 10.8 % / Rmerge(I) obs: 0.151 / Net I/σ(I): 13.7
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 3.9 / Num. unique all: 283 / % possible all: 100

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Processing

Software
NameVersionClassification
APEXdata collection
PHASERphasing
REFMAC5.6.0117refinement
EVAL15data reduction
EVAL15data scaling
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 2W1Y
Resolution: 2.4→55.629 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.937 / SU B: 19.453 / SU ML: 0.233 / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2 / ESU R: 0.555 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.20955 233 4.7 %RANDOM
Rwork0.17563 ---
obs0.1773 4770 99.9 %-
all-8952 --
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: 35.371 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0 Å20 Å2
2---0.49 Å2-0 Å2
3---0.98 Å2
Refinement stepCycle: LAST / Resolution: 2.4→55.629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 13 24 1038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191032
X-RAY DIFFRACTIONr_bond_other_d0.0010.02708
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.9081395
X-RAY DIFFRACTIONr_angle_other_deg0.9493.0091685
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2855128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.562350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.77815166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7031511
X-RAY DIFFRACTIONr_chiral_restr0.0810.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021180
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02235
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: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.18 14 -
Rwork0.177 283 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -20.5239 Å / Origin y: -0.6589 Å / Origin z: -9.237 Å
111213212223313233
T0.0223 Å2-0.0021 Å20.0005 Å2-0.0036 Å20.0048 Å2--0.0318 Å2
L0.9472 °21.046 °2-0.0198 °2-1.2813 °20.1978 °2--0.3884 °2
S-0.0164 Å °-0.0545 Å °-0.0941 Å °-0.0502 Å °-0.0567 Å °-0.0596 Å °-0.0637 Å °0.0079 Å °0.0731 Å °

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