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- PDB-5hmv: Re refinement of 4mwk. -

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Basic information

Entry
Database: PDB / ID: 5hmv
TitleRe refinement of 4mwk.
ComponentsLysozyme C
KeywordsHYDROLASE / Structural dynamics cisplatin histidine protein
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: 0.98 Å
AuthorsHelliwell, J.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council United Kingdom
Citation
Journal: 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.
#1: Journal: Struct Dyn. / Year: 2014
Title: Structural dynamics of cisplatin binding to histidine in a protein Struct. Dyn. 1, 034701 (2014)
Authors: Tanley, S.W.M. / Helliwell, J.R.
History
DepositionJan 17, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
SupersessionJun 8, 2016ID: 4MWK
Revision 1.1Jul 13, 2016Group: Database references
Revision 1.2Aug 10, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.source / _pdbx_audit_support.funding_organization
Revision 1.4Aug 1, 2018Group: Data collection / Database references
Category: citation / citation_author / pdbx_related_exp_data_set
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.title / _citation_author.name / _pdbx_related_exp_data_set.data_reference / _pdbx_related_exp_data_set.data_set_type
Revision 1.5Jan 10, 2024Group: 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 1.6Oct 16, 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)16,32320
Polymers14,2181
Non-polymers2,10519
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-157 kcal/mol
Surface area6760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.998, 31.807, 34.072
Angle α, β, γ (deg.)89.08, 72.00, 67.81
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: 14218.001 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: egg white / References: UniProt: P00698, lysozyme

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Non-polymers , 5 types, 175 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


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


Mass: 62.005 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: NO3
#4: Chemical
ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Pt
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.8 Å3/Da / Density % sol: 31.68 %
Crystal growTemperature: 294 K / Method: batch mode / pH: 4.7
Details: 40MG HEWL CO-CRYSTALLISED WITH 2.6MG CISPLATIN, WITH THE PLATINUM COMPOUNDS BEING IN A 3-FOLD MOLAR EXCESS TO THE PROTEIN. 462.5 MicroL OF A 0.02M NAAC SOLUTION ALONG WITH 462.5 MicroL OF A ...Details: 40MG HEWL CO-CRYSTALLISED WITH 2.6MG CISPLATIN, WITH THE PLATINUM COMPOUNDS BEING IN A 3-FOLD MOLAR EXCESS TO THE PROTEIN. 462.5 MicroL OF A 0.02M NAAC SOLUTION ALONG WITH 462.5 MicroL OF A 0.5M NANO3 SOLUTION WAS USED WITH 75 MicroL DMSO ADDED, BATCH, PH 4.7, EVAPORATION, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Dec 7, 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: 0.98→29.28 Å / Num. obs: 48959 / % possible obs: 94.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 15.6
Reflection shellResolution: 0.98→1.02 Å / Redundancy: 0.6 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 3.2 / % possible all: 49.7

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Processing

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

4mwk
PDB Unreleased entry


Resolution: 0.98→29.28 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.537 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14652 2646 5.1 %RANDOM
Rwork0.12372 ---
obs0.12489 48959 90.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20.1 Å2
2--0.07 Å2-0.05 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 0.98→29.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms992 0 49 156 1197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191071
X-RAY DIFFRACTIONr_bond_other_d0.0010.021003
X-RAY DIFFRACTIONr_angle_refined_deg1.9751.9211442
X-RAY DIFFRACTIONr_angle_other_deg0.9453.0072243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7615132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.3423.13751
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.41615170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5821511
X-RAY DIFFRACTIONr_chiral_restr0.1420.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021264
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02277
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_it0.8630.562525
X-RAY DIFFRACTIONr_mcbond_other0.8620.559524
X-RAY DIFFRACTIONr_mcangle_it1.080.853658
X-RAY DIFFRACTIONr_mcangle_other1.0790.855659
X-RAY DIFFRACTIONr_scbond_it2.0620.774546
X-RAY DIFFRACTIONr_scbond_other2.0610.774538
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.21.097776
X-RAY DIFFRACTIONr_long_range_B_refined2.2916.1851390
X-RAY DIFFRACTIONr_long_range_B_other2.296.1871391
X-RAY DIFFRACTIONr_rigid_bond_restr9.81332074
X-RAY DIFFRACTIONr_sphericity_free13.159527
X-RAY DIFFRACTIONr_sphericity_bonded5.29152196
LS refinement shellResolution: 0.98→1.005 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 90 -
Rwork0.17 2030 -
obs--49.7 %

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