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- PDB-7q0v: Lysozyme soaked with V(IV)OSO4 and phen -

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Basic information

Entry
Database: PDB / ID: 7q0v
TitleLysozyme soaked with V(IV)OSO4 and phen
ComponentsLysozyme
KeywordsHYDROLASE / Protein-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
ACETATE ION / OXYGEN ATOM / 1,10-PHENANTHROLINE / VANADIUM ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsSantos, M.F.A. / Fernandes, A.C.P. / Correia, I. / Sciortino, G. / Garribba, E. / Santos-Silva, T. / Pessoa, J.C.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a Tecnologia Portugal
CitationJournal: Chemistry / Year: 2022
Title: Binding of V IV O 2+ , V IV OL, V IV OL 2 and V V O 2 L Moieties to Proteins: X-ray/Theoretical Characterization and Biological Implications.
Authors: Santos, M.F.A. / Sciortino, G. / Correia, I. / Fernandes, A.C.P. / Santos-Silva, T. / Pisanu, F. / Garribba, E. / Costa Pessoa, J.
History
DepositionOct 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 15, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jul 27, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.4Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,02615
Polymers14,3311
Non-polymers69514
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-74 kcal/mol
Surface area6700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.680, 77.680, 37.757
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-330-

HOH

21A-375-

HOH

31A-445-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lysozyme


Mass: 14331.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli) / References: UniProt: P00698, lysozyme

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Non-polymers , 7 types, 170 molecules

#2: Chemical ChemComp-PHN / 1,10-PHENANTHROLINE


Mass: 180.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H8N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-V / VANADIUM ION


Mass: 50.941 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: V / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: 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 ligand of interestY
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: 1.99 Å3/Da / Density % sol: 38.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 4-8% (M/V) NACL IN 0.1 M ACETATE BUFFER PH 4.5. PROTEIN STOCK CONCENTRATION OF 50 MG/ML.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.12→38.84 Å / Num. obs: 44798 / % possible obs: 99.6 % / Redundancy: 9.9 % / CC1/2: 1 / Net I/σ(I): 21.3
Reflection shellResolution: 1.12→1.14 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2077 / CC1/2: 0.745

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 193L

193l


Resolution: 1.12→38.84 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.47 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17557 2272 5.1 %RANDOM
Rwork0.14736 ---
obs0.14877 42467 99.54 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.295 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å20 Å20 Å2
2---1.17 Å20 Å2
3---2.34 Å2
Refinement stepCycle: LAST / Resolution: 1.12→38.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 42 156 1199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191097
X-RAY DIFFRACTIONr_bond_other_d0.0030.02962
X-RAY DIFFRACTIONr_angle_refined_deg1.5491.8351507
X-RAY DIFFRACTIONr_angle_other_deg1.3062.8992222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0595138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63922.90955
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7215176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6621513
X-RAY DIFFRACTIONr_chiral_restr0.1090.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021273
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02258
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_it1.2131.552531
X-RAY DIFFRACTIONr_mcbond_other1.2141.551530
X-RAY DIFFRACTIONr_mcangle_it1.6342.34677
X-RAY DIFFRACTIONr_mcangle_other1.6332.343677
X-RAY DIFFRACTIONr_scbond_it1.8441.883565
X-RAY DIFFRACTIONr_scbond_other1.8421.888566
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2452.718831
X-RAY DIFFRACTIONr_long_range_B_refined4.1320.2491411
X-RAY DIFFRACTIONr_long_range_B_other3.45519.4141369
X-RAY DIFFRACTIONr_rigid_bond_restr3.4732057
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.12→1.149 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.208 169 -
Rwork0.24 2936 -
obs--94.98 %

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