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- PDB-6dn7: SPRY domain-containing SOCS box protein 2 complexed with WDINNN(B... -

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Basic information

Entry
Database: PDB / ID: 6dn7
TitleSPRY domain-containing SOCS box protein 2 complexed with WDINNN(BAL) Cyclic peptide inhibitor
Components
  • SPRY domain-containing SOCS box protein 4
  • WDINNN(BAL) Cyclic peptide inhibitor
KeywordsIMMUNE SYSTEM/INHIBITOR / proteasomal degradation / nitric oxide / inhibitor / IMMUNE SYSTEM / IMMUNE SYSTEM-INHIBITOR complex
Function / homology
Function and homology information


positive regulation of protein polyubiquitination / SCF ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / regulation of circadian rhythm / rhythmic process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination ...positive regulation of protein polyubiquitination / SCF ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / regulation of circadian rhythm / rhythmic process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / intracellular signal transduction / cytosol
Similarity search - Function
SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily ...SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
WDINNN(BAL) Cyclic peptide inhibitor / SPRY domain-containing SOCS box protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 Å
AuthorsLaw, R.H.P. / Caradoc-Davies, T.T. / Norton, R.S.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1099428 Australia
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: A Cyclic Peptide Inhibitor of the iNOS-SPSB Protein-Protein Interaction as a Potential Anti-Infective Agent.
Authors: Sadek, M.M. / Barlow, N. / Leung, E.W.W. / Williams-Noonan, B.J. / Yap, B.K. / Shariff, F.M. / Caradoc-Davies, T.T. / Nicholson, S.E. / Chalmers, D.K. / Thompson, P.E. / Law, R.H.P. / Norton, R.S.
History
DepositionJun 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SPRY domain-containing SOCS box protein 4
B: WDINNN(BAL) Cyclic peptide inhibitor
C: SPRY domain-containing SOCS box protein 4
D: WDINNN(BAL) Cyclic peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2196
Polymers52,1494
Non-polymers712
Water11,530640
1
A: SPRY domain-containing SOCS box protein 4
hetero molecules

D: WDINNN(BAL) Cyclic peptide inhibitor


Theoretical massNumber of molelcules
Total (without water)26,1103
Polymers26,0742
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area630 Å2
ΔGint-11 kcal/mol
Surface area9670 Å2
2
C: SPRY domain-containing SOCS box protein 4
hetero molecules

B: WDINNN(BAL) Cyclic peptide inhibitor


Theoretical massNumber of molelcules
Total (without water)26,1103
Polymers26,0742
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area630 Å2
ΔGint-12 kcal/mol
Surface area9230 Å2
Unit cell
Length a, b, c (Å)54.690, 65.440, 69.180
Angle α, β, γ (deg.)90.00, 103.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SPRY domain-containing SOCS box protein 4 / SSB-4


Mass: 25228.396 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPSB4, SSB4 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / References: UniProt: Q96A44
#2: Protein/peptide WDINNN(BAL) Cyclic peptide inhibitor


Type: Cyclic peptide / Class: Inhibitor / Mass: 845.857 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: WDINNN(BAL) Cyclic peptide inhibitor
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 640 / Source method: isolated from a natural source / Formula: H2O

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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: 2.31 Å3/Da / Density % sol: 46.72 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 0.2 M Magnesium chloride hexahydrate 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.4→32.61 Å / Num. obs: 91682 / % possible obs: 98.3 % / Redundancy: 4.1 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.031 / Net I/σ(I): 12.7
Reflection shellResolution: 1.4→1.48 Å / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 2.4 / Rpim(I) all: 0.324

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 1.4→32.61 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.946 / SU R Cruickshank DPI: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.068 / SU Rfree Blow DPI: 0.066 / SU Rfree Cruickshank DPI: 0.062
RfactorNum. reflection% reflectionSelection details
Rfree0.213 4651 5.07 %RANDOM
Rwork0.197 ---
obs0.198 91680 98.3 %-
Displacement parametersBiso mean: 21.62 Å2
Baniso -1Baniso -2Baniso -3
1-3.4322 Å20 Å2-0.1252 Å2
2---5.8844 Å20 Å2
3---2.4521 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: 1 / Resolution: 1.4→32.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3134 0 12 642 3788
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013327HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.024540HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1113SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes75HARMONIC2
X-RAY DIFFRACTIONt_gen_planes505HARMONIC5
X-RAY DIFFRACTIONt_it3327HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.59
X-RAY DIFFRACTIONt_other_torsion13.4
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion399SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4503SEMIHARMONIC4
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2591 369 5.44 %
Rwork0.2224 6412 -
all0.2244 6781 -
obs--98.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9593-0.0055-0.07330.41730.10670.9404-0.01510.0240.0411-0.00320.0227-0.0506-0.00820.1337-0.0076-0.01080.0026-0.0152-0.0313-0.0013-0.0448-1.82358.401132.8364
20.7699-0.07460.22040.3319-0.51982.8251-0.0515-0.24980.03350.04240.1240.0379-0.1583-0.6204-0.0725-0.05960.0388-0.00650.1020.0061-0.106221.90797.68259.4832
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ C|* }

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