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- PDB-1xs0: Structure of the E. coli Ivy protein -

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Basic information

Entry
Database: PDB / ID: 1xs0
TitleStructure of the E. coli Ivy protein
ComponentsInhibitor of vertebrate lysozyme
KeywordsHYDROLASE INHIBITOR / alpha beta fold / dimer
Function / homology
Function and homology information


lysozyme inhibitor activity / negative regulation of catalytic activity / : / outer membrane-bounded periplasmic space / periplasmic space / protein homodimerization activity
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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Inhibitor of vertebrate lysozyme / Inhibitor of vertebrate lysozyme
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.58 Å
AuthorsAbergel, C. / Monchois, V. / Byrn, D. / Lazzaroni, J.C. / Claverie, J.M.
Citation
Journal: 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.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: Escherichia coli ykfE ORFan gene encodes a potent inhibitor of C-type lysozyme
Authors: Monchois, V. / Abergel, C. / Sturgis, J. / Jeudy, S. / Claverie, J.M.
#2: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2000
Title: Crystallization and preliminary crystallographic study of b0220, an 'ORFan' protein of unknown function from Escherichia coli
Authors: Abergel, C. / Monchois, V. / Chenivesse, S. / Jeudy, S. / Claverie, J.M.
History
DepositionOct 18, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inhibitor of vertebrate lysozyme
B: Inhibitor of vertebrate lysozyme
C: Inhibitor of vertebrate lysozyme


Theoretical massNumber of molelcules
Total (without water)45,1823
Polymers45,1823
Non-polymers00
Water5,441302
1
A: Inhibitor of vertebrate lysozyme

A: Inhibitor of vertebrate lysozyme


Theoretical massNumber of molelcules
Total (without water)30,1222
Polymers30,1222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
2
B: Inhibitor of vertebrate lysozyme
C: Inhibitor of vertebrate lysozyme


Theoretical massNumber of molelcules
Total (without water)30,1222
Polymers30,1222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-9 kcal/mol
Surface area12420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.339, 46.962, 88.044
Angle α, β, γ (deg.)90.00, 89.95, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-240-

HOH

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Components

#1: Protein Inhibitor of vertebrate lysozyme


Mass: 15060.833 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: PQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P45502, UniProt: P0AD59*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 1.99 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.75
Details: 1.4M sodium citrate, 8% PEG 8000, 20mM TRIS, 50mM NaCl, pH 6.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97917, 0.97941, 0.97393
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 30, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979171
20.979411
30.973931
ReflectionResolution: 1.58→40.7 Å / Num. all: 44577 / Num. obs: 44577 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 9.3 / Redundancy: 3 % / Biso Wilson estimate: 25.7 Å2 / Rsym value: 0.037
Reflection shellResolution: 1.58→1.67 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 3539 / Rsym value: 0.223 / % possible all: 98.1

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.58→14.52 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 823714.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 4496 10.1 %RANDOM
Rwork0.225 ---
obs0.225 37575 97.3 %-
all-37575 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.5474 Å2 / ksol: 0.390667 e/Å3
Displacement parametersBiso mean: 29.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.42 Å20 Å20 Å2
2--2.01 Å20 Å2
3----4.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.58→14.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2942 0 0 302 3244
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.025
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_improper_angle_d1.26
LS refinement shellResolution: 1.58→1.68 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.293 731 9.8 %
Rwork0.26 6705 -
obs-44577 98 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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