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- PDB-6iqo: Se-Met L45M Programmed Cell Death 5 protein from Sulfolobus solfa... -

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Basic information

Entry
Database: PDB / ID: 6iqo
TitleSe-Met L45M Programmed Cell Death 5 protein from Sulfolobus solfataricus
ComponentsDNA-binding protein SSO0352
KeywordsDNA BINDING PROTEIN / Sulfolobus / programmed cell death
Function / homologyDNA-binding protein, archaeal / PDCD5-like / PDCD5-like superfamily / Double-stranded DNA-binding domain / DNA binding / cytosol / DNA-binding protein SSO0352
Function and homology information
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.11 Å
AuthorsChen, C.Y. / Lin, K.F. / Hsu, C.Y. / Tsai, M.J.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (Taiwan) Taiwan
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2019
Title: Crystal structure of the programmed cell death 5 protein from Sulfolobus solfataricus.
Authors: Lin, K.F. / Hsu, J.Y. / Hsieh, D.L. / Tsai, M.J. / Yeh, C.H. / Chen, C.Y.
History
DepositionNov 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: DNA-binding protein SSO0352
B: DNA-binding protein SSO0352
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4523
Polymers30,0382
Non-polymers4141
Water1,35175
1
A: DNA-binding protein SSO0352


Theoretical massNumber of molelcules
Total (without water)15,0191
Polymers15,0191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA-binding protein SSO0352
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4332
Polymers15,0191
Non-polymers4141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.085, 40.860, 77.819
Angle α, β, γ (deg.)90.00, 129.73, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 8 - 104 / Label seq-ID: 8 - 104

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

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Components

#1: Protein DNA-binding protein SSO0352


Mass: 15018.758 Da / Num. of mol.: 2 / Mutation: L45M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: SSO0352 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: Q980F8
#2: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.25 Å3/Da / Density % sol: 45.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: 0.2 M NaCl, 25 % PEG3350, 0.1 M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 31, 2015
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97999 Å / Relative weight: 1
ReflectionResolution: 2.11→30 Å / Num. obs: 15111 / % possible obs: 98.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 41.07 Å2 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.023 / Rrim(I) all: 0.059 / Χ2: 1.168 / Net I/σ(I): 30.13
Reflection shellResolution: 2.11→2.21 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 4.09 / Num. unique obs: 1410 / CC1/2: 0.928 / Rpim(I) all: 0.168 / Rrim(I) all: 0.414 / Χ2: 1.012 / % possible all: 92.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
PHASERphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.11→19.95 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.896 / SU B: 6.166 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.24 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28385 767 5.1 %RANDOM
Rwork0.22475 ---
obs0.228 14333 97.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.61 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.01 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.11→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1667 0 28 75 1770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131701
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181702
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.6782260
X-RAY DIFFRACTIONr_angle_other_deg1.2791.6253975
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8975199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.61922.435115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.39515373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7011521
X-RAY DIFFRACTIONr_chiral_restr0.0750.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021827
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02312
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_it4.2754.674802
X-RAY DIFFRACTIONr_mcbond_other4.2714.669801
X-RAY DIFFRACTIONr_mcangle_it5.9166.973999
X-RAY DIFFRACTIONr_mcangle_other5.9156.9811000
X-RAY DIFFRACTIONr_scbond_it5.8345.763899
X-RAY DIFFRACTIONr_scbond_other5.8315.766900
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.1728.2621262
X-RAY DIFFRACTIONr_long_range_B_refined12.10456.5721848
X-RAY DIFFRACTIONr_long_range_B_other12.10156.6071849
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2823 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.109→2.164 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 59 -
Rwork0.285 853 -
obs--80.92 %

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