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- PDB-6suj: Mutations in SsgB correlate to longitudinal cell division during ... -

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Basic information

Entry
Database: PDB / ID: 6suj
TitleMutations in SsgB correlate to longitudinal cell division during sporulation of Streptomyces coelicolor
ComponentsSporulation and cell division protein SsgA
KeywordsCELL CYCLE / beta barrel / anti-parallel beta-sheet interfaces / cell division component
Function / homologySporulation-specific cell division protein SsgB / Sporulation-specific cell division protein SsgB superfamily / Streptomyces sporulation and cell division protein, SsgA / cell septum / sporulation resulting in formation of a cellular spore / cell division / PHOSPHATE ION / Sporulation and cell division protein SsgA
Function and homology information
Biological speciesStreptomyces sp. Ag82_O1-9 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsXiao, X.S. / Willemse, J.
CitationJournal: To Be Published
Title: Mutations in SsgB correlate to longitudinal cell division during sporulation of Streptomyces coelicolor
Authors: Xiao, X.S.
History
DepositionSep 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: database_2 / pdbx_database_related
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Sporulation and cell division protein SsgA
BBB: Sporulation and cell division protein SsgA
CCC: Sporulation and cell division protein SsgA
DDD: Sporulation and cell division protein SsgA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3115
Polymers68,2164
Non-polymers951
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-39 kcal/mol
Surface area25960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.933, 93.219, 96.241
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains A B
22Chains A C
33Chains A D
44Chains B C
55Chains B D
66Chains C D

NCS ensembles :
IDDetails
6Chains C D
1Chains A B
2Chains A C
3Chains A D
4Chains B C
5Chains B D

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Components

#1: Protein
Sporulation and cell division protein SsgA


Mass: 17053.934 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. Ag82_O1-9 (bacteria) / Gene: BX279_7474 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3D9WLS9
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.23 Å3/Da / Density % sol: 44.93 %
Crystal growTemperature: 291 K / Method: evaporation
Details: 0.2 M Potassium sodium tartrate, 0.1 M Bis-tris prop (pH 7.5), 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.975 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2017
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.56→67.9 Å / Num. obs: 20149 / % possible obs: 99.6 % / Redundancy: 12.1 % / CC1/2: 0.991 / Rmerge(I) obs: 0.446 / Rpim(I) all: 0.134 / Rrim(I) all: 0.466 / Net I/σ(I): 4.8
Reflection shellResolution: 2.56→2.61 Å / Redundancy: 8.4 % / Rmerge(I) obs: 3.642 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 20149 / CC1/2: 0.56 / Rpim(I) all: 1.344 / Rrim(I) all: 3.894 / % possible all: 91.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SLC

6slc


Resolution: 3.2→48.167 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.896 / SU B: 25.916 / SU ML: 0.442 / Cross valid method: FREE R-VALUE / ESU R Free: 0.604
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2935 550 5.226 %
Rwork0.2365 --
all0.239 --
obs-10524 99.744 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.295 Å2
Baniso -1Baniso -2Baniso -3
1--3.65 Å20 Å20 Å2
2--9.239 Å20 Å2
3----5.588 Å2
Refinement stepCycle: LAST / Resolution: 3.2→48.167 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3866 0 5 96 3967
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133971
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173606
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.6455428
X-RAY DIFFRACTIONr_angle_other_deg1.2191.5668333
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6585505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.31619.903206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.45115575
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1221537
X-RAY DIFFRACTIONr_chiral_restr0.0680.2514
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024505
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02862
X-RAY DIFFRACTIONr_nbd_refined0.20.2670
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.23286
X-RAY DIFFRACTIONr_nbtor_refined0.1490.21827
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21968
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.296
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.4840.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2680.230
X-RAY DIFFRACTIONr_nbd_other0.2440.283
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2920.28
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1680.21
X-RAY DIFFRACTIONr_mcbond_it2.8864.2552035
X-RAY DIFFRACTIONr_mcbond_other2.8744.2542034
X-RAY DIFFRACTIONr_mcangle_it4.9926.3712535
X-RAY DIFFRACTIONr_mcangle_other4.9936.3732536
X-RAY DIFFRACTIONr_scbond_it3.0294.6111936
X-RAY DIFFRACTIONr_scbond_other3.0294.6141937
X-RAY DIFFRACTIONr_scangle_it5.096.7622893
X-RAY DIFFRACTIONr_scangle_other5.0896.7652894
X-RAY DIFFRACTIONr_lrange_it10.02379.31814915
X-RAY DIFFRACTIONr_lrange_other10.02379.31714916
X-RAY DIFFRACTIONr_ncsr_local_group_10.1310.053529
X-RAY DIFFRACTIONr_ncsr_local_group_20.1630.053182
X-RAY DIFFRACTIONr_ncsr_local_group_30.1480.053215
X-RAY DIFFRACTIONr_ncsr_local_group_40.1450.053239
X-RAY DIFFRACTIONr_ncsr_local_group_50.1360.053249
X-RAY DIFFRACTIONr_ncsr_local_group_60.1180.053415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.2830.361290.264715X-RAY DIFFRACTION99.8658
3.283-3.3730.284380.26703X-RAY DIFFRACTION100
3.373-3.470.377470.273685X-RAY DIFFRACTION99.8636
3.47-3.5770.287370.243683X-RAY DIFFRACTION100
3.577-3.6940.306400.224629X-RAY DIFFRACTION100
3.694-3.8230.312250.214632X-RAY DIFFRACTION99.6965
3.823-3.9670.225230.219619X-RAY DIFFRACTION99.8445
3.967-4.1280.362320.211574X-RAY DIFFRACTION100
4.128-4.3110.291390.208566X-RAY DIFFRACTION99.835
4.311-4.520.171160.187547X-RAY DIFFRACTION99.47
4.52-4.7640.273320.201509X-RAY DIFFRACTION99.8155
4.764-5.0510.204500.207461X-RAY DIFFRACTION100
5.051-5.3980.411180.238469X-RAY DIFFRACTION99.3878
5.398-5.8270.265240.254446X-RAY DIFFRACTION99.7877
5.827-6.3780.274350.238384X-RAY DIFFRACTION99.7619
6.378-7.1230.4190.27361X-RAY DIFFRACTION99.4764
7.123-8.2090.391140.269334X-RAY DIFFRACTION99.4286
8.209-10.0170.41380.253290X-RAY DIFFRACTION99.3333
10.017-14.010.25180.277221X-RAY DIFFRACTION98.7603
14.01-48.1670.46360.391144X-RAY DIFFRACTION98.0392

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