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- PDB-4gcf: Room temperature X-ray diffraction study of a 6-fold molar excess... -

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Basic information

Entry
Database: PDB / ID: 4gcf
TitleRoom temperature X-ray diffraction study of a 6-fold molar excess of a cisplatin/carboplatin mixture binding to HEWL, Dataset 4
ComponentsLysozyme C
KeywordsHYDROLASE / cisplatin / carboplatin / histidine / relative toxicity / binding occupancy / X-ray radiation damage / radiation therapy / temperature variation and structure
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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsHelliwell, J.R. / Tanley, S.W.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: The crystal structure analysis of the relative binding of cisplatin and carboplatin in a mixture with histidine in a protein studied at 100 and 300 K with repeated X-ray irradiation.
Authors: Helliwell, J.R. / Tanley, S.W.
History
DepositionJul 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2013Provider: 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 / 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 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)14,7994
Polymers14,3311
Non-polymers4683
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.870, 79.870, 37.768
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-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pt
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
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: 2.09 Å3/Da / Density % sol: 41.22 %
Crystal growTemperature: 277 K / pH: 4.7
Details: 49 mg HEWL (3.2 mM), 3 mg cisplatin (10 mM), 3.7 mg carboplatin (10 mM) in 0.04 M sodium acetate buffer (462.5 uL) + 10% sodium chloride precipitant (462.5 uL) + 1 mM DMSO (75 uL), pH 4.7, ...Details: 49 mg HEWL (3.2 mM), 3 mg cisplatin (10 mM), 3.7 mg carboplatin (10 mM) in 0.04 M sodium acetate buffer (462.5 uL) + 10% sodium chloride precipitant (462.5 uL) + 1 mM DMSO (75 uL), pH 4.7, BATCH, temperature 277K

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å
DetectorType: APEX II CCD / Detector: CCD / Date: May 25, 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: 3.5→56.47 Å / Num. all: 1655 / Num. obs: 1655 / % possible obs: 100 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 19.8 % / Rmerge(I) obs: 0.285 / Net I/σ(I): 12.1
Reflection shellResolution: 3.5→3.6 Å / Redundancy: 19.6 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 4.8 / % possible all: 97.5

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Processing

Software
NameVersionClassification
APEXdata collection
PHASERMRphasing
REFMAC5.7.0029refinement
APEXdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W1Y

2w1y


Resolution: 3.5→35.74 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.89 / SU B: 60.534 / SU ML: 0.439 / Cross valid method: THROUGHOUT / ESU R Free: 0.652 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23454 79 4.6 %RANDOM
Rwork0.1695 ---
obs0.17244 1649 99.77 %-
all-1655 --
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: 50.385 Å2
Baniso -1Baniso -2Baniso -3
1--2.14 Å2-0 Å2-0 Å2
2---2.14 Å2-0 Å2
3---4.28 Å2
Refinement stepCycle: LAST / Resolution: 3.5→35.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 6 0 1007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191028
X-RAY DIFFRACTIONr_bond_other_d0.0010.02954
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.9051392
X-RAY DIFFRACTIONr_angle_other_deg0.8523.0072160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.095128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.9912350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4715166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0511511
X-RAY DIFFRACTIONr_chiral_restr0.0710.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021206
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02271
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: 3.498→3.589 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 6 -
Rwork0.198 111 -
obs--99.15 %
Refinement TLS params.Method: refined / Origin x: -20.8235 Å / Origin y: -0.4882 Å / Origin z: -9.3982 Å
111213212223313233
T0.1121 Å2-0.0069 Å2-0.0077 Å2-0.0995 Å2-0.0277 Å2--0.0666 Å2
L2.8541 °21.8841 °20.9602 °2-3.9399 °21.3428 °2--2.6851 °2
S0.0133 Å °0.1266 Å °-0.3928 Å °0.0671 Å °-0.0356 Å °-0.1688 Å °-0.1396 Å °0.105 Å °0.0224 Å °

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