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- PDB-4dd1: EVAL processed HEWL, cisplatin aqueous paratone -

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Basic information

Entry
Database: PDB / ID: 4dd1
TitleEVAL processed HEWL, cisplatin aqueous paratone
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
2-methylprop-1-ene / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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

Downloads & links

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Assembly

Deposited unit
A: Lysozyme C
B: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,16711
Polymers28,6622
Non-polymers5059
Water3,009167
1
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5565
Polymers14,3311
Non-polymers2244
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6126
Polymers14,3311
Non-polymers2815
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.887, 78.703, 37.074
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 1 - 129 / Label seq-ID: 1 - 129

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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.: 2 / 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-MEB / 2-methylprop-1-ene


Mass: 56.106 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 1.98 Å3/Da / Density % sol: 37.95 %
Crystal growTemperature: 295 K / pH: 4.7
Details: HEWL co-crystallized with cisplatin in 1 mL 0.05 M sodium acetate buffer and 1 mL 10% sodium chloride aqueous media, pH 4.7, BATCH, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Nov 26, 2010 / Details: Incoatec Helios confocal optics
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: 1.7→18.04 Å / Num. all: 25216 / Num. obs: 23888 / % possible obs: 94.7 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.9
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 5 / Num. unique all: 1471 / % possible all: 93.6

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Processing

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

2w1y


Resolution: 1.7→18.04 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.1 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2 / ESU R: 0.127 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22654 1284 5.1 %RANDOM
Rwork0.1894 ---
obs0.19126 23888 97.47 %-
all-25216 --
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: 15.643 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→18.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 36 167 2205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192083
X-RAY DIFFRACTIONr_bond_other_d0.0040.021427
X-RAY DIFFRACTIONr_angle_refined_deg2.0541.9162811
X-RAY DIFFRACTIONr_angle_other_deg1.3283.0093403
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2485256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24123100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.65615332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.61522
X-RAY DIFFRACTIONr_chiral_restr0.1470.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022344
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02470
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRms dev position (Å)Weight position
11A5101X-RAY DIFFRACTION0.020.05
12B5101X-RAY DIFFRACTION0.020.05
LS refinement shellResolution: 1.7→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 100 -
Rwork0.177 1471 -
obs--90.18 %

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