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- PDB-5i5q: Re refinement of 4mwn. -

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Basic information

Entry
Database: PDB / ID: 5i5q
TitleRe refinement of 4mwn.
ComponentsLysozyme C
KeywordsHYDROLASE / Structural dynamics / cisplatin / histidine
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
NITRATE ION / : / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsHelliwell, 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 15, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
SupersessionJun 8, 2016ID: 4mwn
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: citation / pdbx_related_exp_data_set
Item: _citation.journal_abbrev / _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
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)15,1818
Polymers14,3311
Non-polymers8497
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-57 kcal/mol
Surface area6490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.346, 32.134, 34.296
Angle α, β, γ (deg.)88.04, 71.17, 68.35
Int Tables number1
Space group name H-MP1

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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) / Tissue: egg white / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Pt
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 1.84 Å3/Da / Density % sol: 33.2 %
Crystal growTemperature: 294 K / Method: batch mode / pH: 4.7
Details: CRYSTALLIZATION CONDITIONS: 40MG HEWL CO-CRYSTALLISED WITH 2.6MG CISPLATIN, WITH THE PLATINUM COMPOUNDS BEING IN A 3-FOLD MOLAR EXCESS TO THE PROTEIN, 462.5 UL OF A 0.02M NAAC SOLUTION ALONG ...Details: CRYSTALLIZATION CONDITIONS: 40MG HEWL CO-CRYSTALLISED WITH 2.6MG CISPLATIN, WITH THE PLATINUM COMPOUNDS BEING IN A 3-FOLD MOLAR EXCESS TO THE PROTEIN, 462.5 UL OF A 0.02M NAAC SOLUTION ALONG WITH 462.5 UL OF A 0.5M NANO3 SOLUTION WAS USED WITH 75 UL DMSO ADDED, BATCH, PH 4.7, EVAPORATION, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Dec 15, 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: 1.42→32.31 Å / Num. obs: 18176 / % possible obs: 94.8 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 6.8
Reflection shellResolution: 1.42→1.51 Å / Redundancy: 2 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 1.1 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
SAINTdata reduction
APEXdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4mwn

4mwn
PDB Unreleased entry


Resolution: 1.42→32.31 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.252 / SU ML: 0.058 / SU R Cruickshank DPI: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.083 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23687 984 5.1 %RANDOM
Rwork0.18462 ---
obs0.18734 18176 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.451 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.28 Å2-0.13 Å2
2---0.26 Å2-0.02 Å2
3---0.24 Å2
Refinement stepCycle: 1 / Resolution: 1.42→32.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms992 0 19 37 1048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191038
X-RAY DIFFRACTIONr_bond_other_d0.0010.02970
X-RAY DIFFRACTIONr_angle_refined_deg1.8941.9081403
X-RAY DIFFRACTIONr_angle_other_deg1.0013.0072172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4825129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.05423.13751
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.90515166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6441511
X-RAY DIFFRACTIONr_chiral_restr0.1240.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021225
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02272
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_it2.1731.211516
X-RAY DIFFRACTIONr_mcbond_other2.1231.206515
X-RAY DIFFRACTIONr_mcangle_it2.3121.821645
X-RAY DIFFRACTIONr_mcangle_other2.3261.826646
X-RAY DIFFRACTIONr_scbond_it3.4661.646522
X-RAY DIFFRACTIONr_scbond_other3.3831.635514
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5452.291750
X-RAY DIFFRACTIONr_long_range_B_refined3.31711.0351210
X-RAY DIFFRACTIONr_long_range_B_other3.29510.9321200
X-RAY DIFFRACTIONr_rigid_bond_restr5.36932008
X-RAY DIFFRACTIONr_sphericity_free22.052517
X-RAY DIFFRACTIONr_sphericity_bonded7.43552010
LS refinement shellResolution: 1.42→1.457 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 80 -
Rwork0.233 1356 -
obs--98.49 %

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