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- PDB-6jwn: Crystal structure of the SPRY domain of SPSB2 in complex with cR9... -

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Basic information

Entry
Database: PDB / ID: 6jwn
TitleCrystal structure of the SPRY domain of SPSB2 in complex with cR9, a cyclic peptide inhibitor of SPSB-iNOS interaction
Components
  • Nitric oxide synthase, inducible
  • SPRY domain-containing SOCS box protein 2
KeywordsPROTEIN BINDING/INHIBITOR / PRY-SPRY / B30.2 / E3 ubiquitin ligase / inducible nitric oxide synthase / PROTEIN BINDING-INHIBITOR complex
Function / homology
Function and homology information


positive regulation of leukocyte mediated cytotoxicity / Inhibition of nitric oxide production / peptidyl-cysteine S-nitrosylation / regulation of cellular respiration / Nitric oxide stimulates guanylate cyclase / prostaglandin secretion / ROS and RNS production in phagocytes / tetrahydrobiopterin binding / arginine binding / SCF ubiquitin ligase complex ...positive regulation of leukocyte mediated cytotoxicity / Inhibition of nitric oxide production / peptidyl-cysteine S-nitrosylation / regulation of cellular respiration / Nitric oxide stimulates guanylate cyclase / prostaglandin secretion / ROS and RNS production in phagocytes / tetrahydrobiopterin binding / arginine binding / SCF ubiquitin ligase complex / superoxide metabolic process / cortical cytoskeleton / regulation of cytokine production involved in inflammatory response / Fc-gamma receptor signaling pathway involved in phagocytosis / peroxisomal matrix / nitric oxide mediated signal transduction / nitric-oxide synthase (NADPH) / nitric-oxide synthase activity / ubiquitin-like ligase-substrate adaptor activity / L-arginine catabolic process / negative regulation of blood pressure / response to hormone / nitric oxide biosynthetic process / regulation of insulin secretion / innate immune response in mucosa / cell redox homeostasis / positive regulation of interleukin-8 production / response to bacterium / Peroxisomal protein import / negative regulation of protein catabolic process / cellular response to type II interferon / positive regulation of interleukin-6 production / circadian rhythm / peroxisome / Antigen processing: Ubiquitination & Proteasome degradation / cellular response to xenobiotic stimulus / FMN binding / flavin adenine dinucleotide binding / NADP binding / regulation of cell population proliferation / Neddylation / cellular response to lipopolysaccharide / ubiquitin-dependent protein catabolic process / defense response to Gram-negative bacterium / Interleukin-4 and Interleukin-13 signaling / response to lipopolysaccharide / proteasome-mediated ubiquitin-dependent protein catabolic process / response to hypoxia / calmodulin binding / intracellular signal transduction / protein ubiquitination / defense response to bacterium / inflammatory response / negative regulation of gene expression / heme binding / perinuclear region of cytoplasm / protein homodimerization activity / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
SSB2, SOCS box domain / : / suppressors of cytokine signalling / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / SPRY domain / B30.2/SPRY domain ...SSB2, SOCS box domain / : / suppressors of cytokine signalling / 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. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Nitric-oxide synthase, eukaryote / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily / : / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase (NOS) signature. / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Flavoprotein-like superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Nitric oxide synthase, inducible / SPRY domain-containing SOCS box protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsLi, K. / Kuang, Z.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31270817 China
National Natural Science Foundation of China81571539 China
Ministry of Education (China)21617443 China
CitationJournal: To Be Published
Title: Crystal structure of SPSB2 in complex with cR9, a cyclic peptide inhibitor of SPSB-iNOS interaction
Authors: Li, K. / Kuang, Z.
History
DepositionApr 21, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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 2
B: Nitric oxide synthase, inducible
C: SPRY domain-containing SOCS box protein 2
D: Nitric oxide synthase, inducible


Theoretical massNumber of molelcules
Total (without water)47,8554
Polymers47,8554
Non-polymers00
Water2,468137
1
A: SPRY domain-containing SOCS box protein 2
B: Nitric oxide synthase, inducible


Theoretical massNumber of molelcules
Total (without water)23,9282
Polymers23,9282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint0 kcal/mol
Surface area9210 Å2
MethodPISA
2
C: SPRY domain-containing SOCS box protein 2
D: Nitric oxide synthase, inducible


Theoretical massNumber of molelcules
Total (without water)23,9282
Polymers23,9282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint0 kcal/mol
Surface area9210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.411, 46.386, 61.177
Angle α, β, γ (deg.)87.72, 75.01, 89.92
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 28 - 220 / Label seq-ID: 9 - 201

Dom-IDAuth asym-IDLabel asym-ID
1AA
2CC

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Components

#1: Protein SPRY domain-containing SOCS box protein 2 / SSB-2 / Gene-rich cluster protein C9


Mass: 22896.604 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPSB2, GRCC9, SSB2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99619
#2: Protein/peptide Nitric oxide synthase, inducible / cR9 peptide


Mass: 1031.059 Da / Num. of mol.: 2 / Fragment: UNP residues 21-29 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P35228, nitric-oxide synthase (NADPH)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 1.85 Å3/Da / Density % sol: 33.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.02M Citric acid, 0.08M Bis-Tris propane pH7.6, 14%(w/v0 Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.61→59.05 Å / Num. obs: 42845 / % possible obs: 96.3 % / Redundancy: 5.3 % / Net I/σ(I): 7.6
Reflection shellResolution: 1.61→1.64 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→59.05 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.93 / SU B: 1.792 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.096
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20506 2131 5 %RANDOM
Rwork0.18496 ---
obs0.18598 40695 96.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.634 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0.17 Å2-0.4 Å2
2--0.27 Å20.38 Å2
3----0.15 Å2
Refinement stepCycle: 1 / Resolution: 1.61→59.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3120 0 0 137 3257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0153200
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172770
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.7664342
X-RAY DIFFRACTIONr_angle_other_deg0.5711.7166516
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.185402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.95118.831154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15115432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.71532
X-RAY DIFFRACTIONr_chiral_restr0.0780.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213720
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02592
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_it1.491.2781614
X-RAY DIFFRACTIONr_mcbond_other1.491.2781615
X-RAY DIFFRACTIONr_mcangle_it2.4431.9112014
X-RAY DIFFRACTIONr_mcangle_other2.4481.9122015
X-RAY DIFFRACTIONr_scbond_it2.0911.4961586
X-RAY DIFFRACTIONr_scbond_other2.0851.4951585
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2662.1492329
X-RAY DIFFRACTIONr_long_range_B_refined4.65715.1143339
X-RAY DIFFRACTIONr_long_range_B_other4.66115.0773330
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 6260 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2C
LS refinement shellResolution: 1.611→1.653 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 150 -
Rwork0.198 2723 -
obs--88.32 %

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