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- PDB-4yen: Room temperature X-ray diffraction studies of cisplatin binding t... -

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Basic information

Entry
Database: PDB / ID: 4yen
TitleRoom temperature X-ray diffraction studies of cisplatin binding to HEWL in DMSO media after 14 months of crystal storage - new refinement
ComponentsLysozyme C
KeywordsHYDROLASE / Re-refinement of 4G4A / Cisplatin / Metal binding
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 / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsShabalin, I.G. / Dauter, Z. / Jaskolski, M. / Minor, W. / Wlodawer, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin.
Authors: Shabalin, I. / Dauter, Z. / Jaskolski, M. / Minor, W. / Wlodawer, A.
#1: Journal: 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
DepositionFeb 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Sep 16, 2015Group: Database references
Revision 1.3Nov 4, 2015Group: Database references
Revision 1.4Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.7Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.8Nov 13, 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)14,9779
Polymers14,3311
Non-polymers6468
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.113, 79.113, 37.985
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-303-

HOH

21A-337-

HOH

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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 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.07 Å3/Da / Density % sol: 40.68 %
Crystal growTemperature: 295 K / Method: batch mode / pH: 4.7
Details: HEWL co-crystallized with cisplatin with 5% DMSO media in 1 mL 10% sodium chloride + 1 ml 0.04 M sodium acetate, pH 4.7

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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 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: 2→50 Å / Num. all: 8602 / Num. obs: 8602 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.032 / Rrim(I) all: 0.092 / Rsym value: 0.086 / Χ2: 0.905 / Net I/av σ(I): 19.439 / Net I/σ(I): 8.8 / Num. measured all: 68208
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.035.60.5712.74110.8650.2640.630.691100
2.03-2.075.70.4694140.8890.2140.5160.701100
2.07-2.115.80.434270.8990.1930.4720.744100
2.11-2.1560.3254130.9330.1460.3570.753100
2.15-2.26.10.3384180.9440.1480.370.727100
2.2-2.256.20.2984260.9690.130.3260.772100
2.25-2.316.40.2564170.9620.110.2790.73100
2.31-2.376.50.2664180.970.1120.290.801100
2.37-2.446.90.2554160.9680.1040.2760.816100
2.44-2.527.60.2234270.970.0860.2390.915100
2.52-2.617.80.2024180.9860.0770.2161.002100
2.61-2.717.90.1634390.9860.0620.1750.995100
2.71-2.848.10.1474210.9890.0540.1570.974100
2.84-2.998.30.1314230.9920.0480.141.019100
2.99-3.178.40.0974420.9950.0350.1041.085100
3.17-3.4290.0774270.9970.0270.0821.088100
3.42-3.769.70.064460.9980.020.0631.042100
3.76-4.3111.90.0524420.9990.0160.0551.065100
4.31-5.4312.40.0434560.9990.0120.0450.918100
5.43-50110.03150110.010.0330.75999.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
APEXdata collection
HKL-3000data reduction
HKL-3000data scaling
Cootmodel building
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4G4A

4g4a
PDB Unreleased entry


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.1507 / WRfactor Rwork: 0.1277 / FOM work R set: 0.884 / SU B: 6.737 / SU ML: 0.093 / SU R Cruickshank DPI: 0.161 / SU Rfree: 0.1334 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS This deposit resulted from an analysis of a number of PDB entries that contain cisplatin or carboplatin in complex ...Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS This deposit resulted from an analysis of a number of PDB entries that contain cisplatin or carboplatin in complex with proteins, conducted in the spirit of the Terwilliger-Bricogne motto advocating continuous improvement of the macromolecular models in the PDB (Acta Cryst. D70, 2533, 2014). Since the original data frames for this structure are available at the http://rawdata.chem.uu.nl server, they have been re-processed, and the new structure factors have been used for the present re-refinement. The coordinates originally deposited as 4G4A were used as the starting point for this independent re-refinement. The new model is based on data extending to higher resolution, includes some reinterpretation of the ligands, has lower R factors, and improved statistics describing the agreement with the experimental data.
RfactorNum. reflection% reflectionSelection details
Rfree0.1788 450 5.3 %RANDOM
Rwork0.1464 ---
obs0.1481 8107 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.67 Å2 / Biso mean: 28.046 Å2 / Biso min: 10.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å2-0 Å2
2--0.06 Å2-0 Å2
3----0.12 Å2
Refinement stepCycle: final / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms995 0 11 75 1081
Biso mean--41.28 37.58 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191028
X-RAY DIFFRACTIONr_bond_other_d0.0020.02941
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.9041395
X-RAY DIFFRACTIONr_angle_other_deg1.06932142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3075130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.3223.450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.3415164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5061510
X-RAY DIFFRACTIONr_chiral_restr0.1010.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021214
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02270
X-RAY DIFFRACTIONr_mcbond_it0.9061.515517
X-RAY DIFFRACTIONr_mcbond_other0.9051.513516
X-RAY DIFFRACTIONr_mcangle_it1.542.268645
X-RAY DIFFRACTIONr_sphericity_free25.9950.11
X-RAY DIFFRACTIONr_sphericity_bonded30.5270.16
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 28 -
Rwork0.177 576 -
all-604 -
obs--99.34 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.812-0.0917-0.48623.312-0.01722.0818-0.07920.0256-0.3131-0.18070.0876-0.16050.22030.0952-0.00850.0883-0.00580.02970.0643-0.03950.1034-17.888-8.424-15.817
23.53982.0257-0.22163.71080.34031.4439-0.09210.0777-0.05790.00850.0757-0.0194-0.0410.00920.01640.08370.00620.00650.0792-0.0120.0913-22.3290.27-13.042
32.621.39250.58772.5785-0.10330.7990.1488-0.2126-0.04080.2181-0.1605-0.0161-0.0070.00540.01170.0973-0.01580.01940.08430.00440.0674-18.1393.087-2.72
45.1711-3.3548-3.11946.28384.26546.9954-0.01810.2038-0.3057-0.09740.00710.09270.1922-0.16370.01110.1193-0.0189-0.02960.1009-0.00660.123-29.48-5.794-18.216
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 20
2X-RAY DIFFRACTION2A21 - 45
3X-RAY DIFFRACTION3A46 - 111
4X-RAY DIFFRACTION4A112 - 129

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