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- PDB-1uuz: IVY:A NEW FAMILY OF PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1uuz
TitleIVY:A NEW FAMILY OF PROTEIN
Components
  • INHIBITOR OF VERTEBRATE LYSOZYME
  • LYSOZYME C
KeywordsHYDROLASE/INHIBITOR / LYSOZYME-INHIBITOR COMPLEX / IVY / TYPE-C LYSOZYME INHIBITOR / LYSOZYME / HYDROLASE / GLYCOSIDASE / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


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 / periplasmic space / defense response to Gram-positive bacterium ...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 / periplasmic space / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Inhibitor of vertebrate lysozyme / Inhibitor of vertebrate lysozyme / Inhibitor of vertebrate lysozyme superfamily / Inhibitor of vertebrate lysozyme (Ivy) / Inhibitor of vertebrate lysozyme, Ivy / Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 ...Inhibitor of vertebrate lysozyme / Inhibitor of vertebrate lysozyme / Inhibitor of vertebrate lysozyme superfamily / Inhibitor of vertebrate lysozyme (Ivy) / Inhibitor of vertebrate lysozyme, Ivy / 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 / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Lysozyme C / Inhibitor of vertebrate lysozyme
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
GALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAbergel, C. / Lembo, F. / Byrne, D. / Maza, C. / Claverie, J.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Structure and Evolution of the Ivy Protein Family, Unexpected Lysozyme Inhibitors in Gram-Negative Bacteria.
Authors: Abergel, C. / Monchois, V. / Byrne, D. / Chenivesse, S. / Lembo, F. / Lazzaroni, J.-C. / Claverie, J.M.
History
DepositionJan 12, 2004Deposition site: PDBE / Processing site: PDBE
SupersessionJan 14, 2004ID: 1HKE
Revision 1.0Jan 14, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INHIBITOR OF VERTEBRATE LYSOZYME
B: INHIBITOR OF VERTEBRATE LYSOZYME
C: LYSOZYME C
D: LYSOZYME C


Theoretical massNumber of molelcules
Total (without water)59,7614
Polymers59,7614
Non-polymers00
Water6,954386
1
A: INHIBITOR OF VERTEBRATE LYSOZYME
D: LYSOZYME C


Theoretical massNumber of molelcules
Total (without water)29,8802
Polymers29,8802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: INHIBITOR OF VERTEBRATE LYSOZYME
C: LYSOZYME C


Theoretical massNumber of molelcules
Total (without water)29,8802
Polymers29,8802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)52.346, 60.760, 78.245
Angle α, β, γ (deg.)90.00, 102.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein INHIBITOR OF VERTEBRATE LYSOZYME / IVY


Mass: 15549.329 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: IVY COMPLEXED WITH HEWL IN CRYSTAL / Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Description: C-TERM HIS-TAG / Plasmid: PET26 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9HXB1
#2: Protein LYSOZYME C


Mass: 14331.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: SIGMA / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: P00698, lysozyme
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 386 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE LOOP CKPHDC IS RESPONSIBLE OF THE C-TYPE LYSOZYME ACTIVITY INHIBITION

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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: 2.13 Å3/Da / Density % sol: 42.33 %
Crystal growpH: 6.5
Details: 20% POLYETHYLENEGLYCOL 4000, IMIDAZOLE/MALATE 0.2M PH 6.0, 5% GLYCEROL
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
13.4 mg/mlprotein1drop
220 mMTris1droppH8
30.2 Mimidazole malate1reservoirpH6.0
415-20 %(w/v)PEG40001reservoir
55 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.8→47.673 Å / Num. obs: 42990 / % possible obs: 96.5 % / Redundancy: 2.8 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 7.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 2.3 / % possible all: 96.5
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 25 Å / Redundancy: 2.8 % / Num. measured all: 122164 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
Highest resolution: 1.8 Å / % possible obs: 96.5 % / Redundancy: 2.8 % / Num. unique obs: 4166 / Num. measured obs: 11604 / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GPQ

1gpq


Resolution: 1.8→23.94 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.25 4331 10.1 %RANDOM
Rwork0.213 ---
obs0.213 42946 96.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.456 Å2 / ksol: 0.325439 e/Å3
Displacement parametersBiso mean: 27.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.67 Å20 Å24.45 Å2
2--5.35 Å20 Å2
3----2.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.8→23.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4023 0 0 386 4409
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it1.892
X-RAY DIFFRACTIONc_scbond_it2.052
X-RAY DIFFRACTIONc_scangle_it2.972.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.312 690 9.8 %
Rwork0.27 6382 -
obs--95.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 9.9 % / Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74

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