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- PDB-3chm: Crystal structure of PCI domain from A. thaliana COP9 signalosome... -

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Basic information

Entry
Database: PDB / ID: 3chm
TitleCrystal structure of PCI domain from A. thaliana COP9 signalosome subunit 7 (CSN7)
ComponentsCOP9 signalosome complex subunit 7
KeywordsPLANT PROTEIN / HEAT/ARM repeats / winged helix motif / Developmental protein / Nucleus / Phosphoprotein / Phytochrome signaling pathway / Signalosome
Function / homology
Function and homology information


red, far-red light phototransduction / COP9 signalosome assembly / multicellular organism development / protein deneddylation / COP9 signalosome / cytosol
Similarity search - Function
motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / Proteasome component (PCI) domain / PCI domain profile.
Similarity search - Domain/homology
ACETATE ION / COP9 signalosome complex subunit 7
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsDessau, M. / Hirsch, J.A.
Citation
Journal: Plant Cell / Year: 2008
Title: The Arabidopsis COP9 signalosome subunit 7 is a model PCI domain protein with subdomains involved in COP9 signalosome assembly
Authors: Dessau, M. / Halimi, Y. / Erez, T. / Chomsky-Hecht, O. / Chamovitz, D.A. / Hirsch, J.A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Expression, purification and crystallization of a PCI domain from the COP9 signalosome subunit 7 (CSN7)
Authors: Dessau, M. / Chamovitz, D.A. / Hirsch, J.A.
History
DepositionMar 10, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COP9 signalosome complex subunit 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0306
Polymers18,8051
Non-polymers2265
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.094, 85.796, 72.343
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-398-

HOH

21A-418-

HOH

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Components

#1: Protein COP9 signalosome complex subunit 7 / / CSN complex subunit 7 / Protein FUSCA 5


Mass: 18804.594 Da / Num. of mol.: 1 / Fragment: PCI domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: FUS5 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner DE3 codon(+) / References: UniProt: Q94JU3
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 23% w/v PEG 8000, 0.1M sodium cacodylate (pH 7.2), 0.06-0.08M Mg-acetate tetrahydrate, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-110.934
SYNCHROTRONESRF BM1620.97944, 0.97967
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDNov 30, 2006
MAR CCD 165 mm2CCDSep 20, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9341
20.979441
30.979671
ReflectionResolution: 1.5→50 Å / Num. all: 28989 / Num. obs: 28844 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Rsym value: 0.035 / Net I/σ(I): 47.9
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 6.7 / Num. unique all: 2763 / Rsym value: 0.269 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→36.9 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.198 / SU ML: 0.042 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.071 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19996 1186 4.1 %RANDOM
Rwork0.16413 ---
all0.16559 28708 --
obs0.16559 27494 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.727 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å20 Å2
2--0.35 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.5→36.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1266 0 14 244 1524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221476
X-RAY DIFFRACTIONr_bond_other_d0.0070.02999
X-RAY DIFFRACTIONr_angle_refined_deg1.541.9942023
X-RAY DIFFRACTIONr_angle_other_deg0.99932475
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2885199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.26225.15266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.02815272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.597159
X-RAY DIFFRACTIONr_chiral_restr0.0950.2229
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021718
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02282
X-RAY DIFFRACTIONr_nbd_refined0.230.2342
X-RAY DIFFRACTIONr_nbd_other0.2010.21090
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2739
X-RAY DIFFRACTIONr_nbtor_other0.090.2731
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2205
X-RAY DIFFRACTIONr_metal_ion_refined0.0990.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3310.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2030.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.231
X-RAY DIFFRACTIONr_mcbond_it2.05531222
X-RAY DIFFRACTIONr_mcbond_other0.3343360
X-RAY DIFFRACTIONr_mcangle_it2.23151517
X-RAY DIFFRACTIONr_scbond_it3.4397610
X-RAY DIFFRACTIONr_scangle_it4.51810504
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.174 98 -
Rwork0.176 1932 -
obs-2450 96.25 %
Refinement TLS params.Method: refined / Origin x: -12.2246 Å / Origin y: -1.2859 Å / Origin z: 13.8651 Å
111213212223313233
T-0.0161 Å20 Å2-0.0044 Å2--0.0141 Å20.0096 Å2---0.0266 Å2
L0.6955 °2-0.2296 °2-0.3397 °2-0.4333 °20.1784 °2--0.5314 °2
S0.0019 Å °-0.0307 Å °-0.0227 Å °0.0074 Å °-0.0099 Å °0.0377 Å °0.0436 Å °0.0184 Å °0.008 Å °

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