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- PDB-5idd: Comment on S. W. M. Tanley and J. R. Helliwell Structural dynamic... -

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Basic information

Entry
Database: PDB / ID: 5idd
TitleComment on S. W. M. Tanley and J. R. Helliwell Structural dynamics of cisplatin binding to histidine in a protein Struct. Dyn. 1, 034701 (2014) regarding the refinement of 4mwk, 4mwm, 4mwn and 4oxe and the method we have adopted.
ComponentsLysozyme C
KeywordsHYDROLASE / Structural dynamics carboplatin histidine 200K
Function / homology
Function and homology information


Lactose synthesis / 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 ...Lactose synthesis / 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 / NITRATE ION / : / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsTanley, S.W.M. / Helliwell, J.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council United Kingdom
CitationJournal: Struct Dyn. / Year: 2016
Title: Comment on "Structural dynamics of cisplatin binding to histidine in a protein" [Struct. Dyn. 1, 034701 (2014)].
Authors: Tanley, S.W. / Helliwell, J.R.
History
DepositionFeb 24, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
SupersessionJun 8, 2016ID: 4oxe
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.source / _pdbx_audit_support.funding_organization
Revision 1.3Aug 8, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)15,53415
Polymers14,3311
Non-polymers1,20214
Water1,42379
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-78 kcal/mol
Surface area6820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.957, 31.794, 34.055
Angle α, β, γ (deg.)88.76, 71.99, 68.33
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 6 types, 93 molecules

#2: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PT / PLATINUM (II) ION


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


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 1.79 Å3/Da / Density % sol: 31.29 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 4.7
Details: CRYSTALLIZATION CONDITIONS: 40MG HEWL (2.7MM) CO-CRYSTALLISED WITH 3MG CARBOPLATIN (8.1MM). 462.5 microL OF A 0.02M NAAC SOLUTION ALONG REMARK 280 WITH 462.5 microL OF A 0.5M NANO3 SOLUTION ...Details: CRYSTALLIZATION CONDITIONS: 40MG HEWL (2.7MM) CO-CRYSTALLISED WITH 3MG CARBOPLATIN (8.1MM). 462.5 microL OF A 0.02M NAAC SOLUTION ALONG REMARK 280 WITH 462.5 microL OF A 0.5M NANO3 SOLUTION WAS USED WITH 75 microL DMSO.

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Nov 18, 2012 / Details: CONFOCAL MIRROR OPTICS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.13→32.21 Å / Num. obs: 35817 / % possible obs: 94.1 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 7.2
Reflection shellResolution: 1.13→1.16 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2 / % possible all: 77

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
SAINTdata reduction
APEX 2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4oxe

4oxe
PDB Unreleased entry


Resolution: 1.13→32.21 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.585 / SU ML: 0.034 / SU R Cruickshank DPI: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.047 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21982 1762 5 %RANDOM
Rwork0.1775 ---
obs0.17964 33282 94.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.268 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.13→32.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms986 0 41 79 1106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0191044
X-RAY DIFFRACTIONr_bond_other_d0.0010.02940
X-RAY DIFFRACTIONr_angle_refined_deg2.0561.9181407
X-RAY DIFFRACTIONr_angle_other_deg1.0443.0082130
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9485129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44323.26549
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.15815162
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9421510
X-RAY DIFFRACTIONr_chiral_restr0.1490.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021236
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02268
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_it2.0960.991517
X-RAY DIFFRACTIONr_mcbond_other1.8690.985515
X-RAY DIFFRACTIONr_mcangle_it2.6021.494645
X-RAY DIFFRACTIONr_mcangle_other2.771.499646
X-RAY DIFFRACTIONr_scbond_it3.5261.274527
X-RAY DIFFRACTIONr_scbond_other3.5231.274528
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1311.811763
X-RAY DIFFRACTIONr_long_range_B_refined3.878.9571257
X-RAY DIFFRACTIONr_long_range_B_other3.8698.9611258
X-RAY DIFFRACTIONr_rigid_bond_restr8.79331984
X-RAY DIFFRACTIONr_sphericity_free27.301527
X-RAY DIFFRACTIONr_sphericity_bonded11.11652025
LS refinement shellResolution: 1.13→1.159 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 106 -
Rwork0.257 2035 -
obs--77.77 %

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