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- PDB-5nmo: Structure of the Bacillus subtilis Smc Joint domain -

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Basic information

Entry
Database: PDB / ID: 5nmo
TitleStructure of the Bacillus subtilis Smc Joint domain
ComponentsChromosome partition protein Smc,Chromosome partition protein Smc
KeywordsCELL CYCLE / Smc Chromosome Segregation
Function / homology
Function and homology information


cohesin loader activity / chromosome condensation / mitotic sister chromatid cohesion / chromosome segregation / chromosome / double-stranded DNA binding / DNA replication / ATP hydrolysis activity / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Structural maintenance of chromosomes protein, prokaryotic / Structural maintenance of chromosomes protein / SMCs flexible hinge / SMCs flexible hinge superfamily / SMC proteins Flexible Hinge Domain / SMC proteins Flexible Hinge Domain / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Chromosome partition protein Smc
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.899 Å
AuthorsDiebold-Durand, M.-L. / Basquin, J. / Gruber, S.
Funding support1items
OrganizationGrant numberCountry
European Research Council Starting260853
CitationJournal: Mol. Cell / Year: 2017
Title: Structure of Full-Length SMC and Rearrangements Required for Chromosome Organization.
Authors: Diebold-Durand, M.L. / Lee, H. / Ruiz Avila, L.B. / Noh, H. / Shin, H.C. / Im, H. / Bock, F.P. / Burmann, F. / Durand, A. / Basfeld, A. / Ham, S. / Basquin, J. / Oh, B.H. / Gruber, S.
History
DepositionApr 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Aug 2, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chromosome partition protein Smc,Chromosome partition protein Smc
B: Chromosome partition protein Smc,Chromosome partition protein Smc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,48525
Polymers38,4292
Non-polymers2,05623
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint-147 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.036, 83.865, 64.834
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Chromosome partition protein Smc,Chromosome partition protein Smc


Mass: 19214.719 Da / Num. of mol.: 2 / Fragment: UNP residues 188-253,UNP residues 922-1011
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Gene: smc, ylqA, BSU15940 / Plasmid: pET-22 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P51834

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Non-polymers , 5 types, 114 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 3.08 Å3/Da / Density % sol: 60.04 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 28% pEG 3350 50 mM Tris pH 8.0 8% MPD 180 mM ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.89→51.294 Å / Num. obs: 65454 / % possible obs: 99.7 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 16.95
Reflection shellResolution: 1.81→1.91 Å / Redundancy: 8.27 % / Rmerge(I) obs: 1.688 / Mean I/σ(I) obs: 1.1 / Num. unique all: 5688 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XDSdata scaling
SHELXCDphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.899→51.294 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 23.33
RfactorNum. reflection% reflection
Rfree0.2281 3223 4.98 %
Rwork0.1912 --
obs0.193 64662 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 158.9 Å2 / Biso mean: 68.8334 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 1.899→51.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2379 0 232 91 2702
Biso mean--114.85 55.77 -
Num. residues----298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032531
X-RAY DIFFRACTIONf_angle_d0.6433376
X-RAY DIFFRACTIONf_chiral_restr0.027371
X-RAY DIFFRACTIONf_plane_restr0.002417
X-RAY DIFFRACTIONf_dihedral_angle_d14.262966
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8994-1.92770.36151270.34182615274297
1.9277-1.95780.32411670.319526542821100
1.9578-1.98990.31151580.296926542812100
1.9899-2.02420.28341250.283226862811100
2.0242-2.06110.27291520.268626562808100
2.0611-2.10070.28541460.252226482794100
2.1007-2.14360.28111670.237926492816100
2.1436-2.19020.25571510.230626732824100
2.1902-2.24110.24781340.204526952829100
2.2411-2.29720.25111070.195627102817100
2.2972-2.35930.21371220.189726842806100
2.3593-2.42870.23481540.181126462800100
2.4287-2.50710.20241420.188626722814100
2.5071-2.59670.24121610.187726732834100
2.5967-2.70070.24451010.198127112812100
2.7007-2.82360.21531230.213227032826100
2.8236-2.97240.22921810.220226282809100
2.9724-3.15860.25471620.199226452807100
3.1586-3.40250.25531440.192626812825100
3.4025-3.74480.18921050.174427122817100
3.7448-4.28640.20931190.154926872806100
4.2864-5.39950.19291230.163127082831100
5.3995-51.31220.22011520.18942649280199
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)
19.7048-4.2475-6.61655.57183.92144.8779-0.0659-1.48350.15960.29510.4973-0.4788-0.18780.6784-0.4850.56540.1499-0.0190.78860.00870.489136.06696.1168-28.025
23.8772-4.1864-5.03345.22484.78577.2794-0.2415-0.0172-0.3950.41750.4415-0.02790.61611.1247-0.05220.50580.1958-0.03540.625-0.07560.399215.779817.5569-9.796
32.5537-2.6085-2.96925.435-0.65948.50460.0222-0.18880.2306-0.2850.03520.2002-0.14790.35120.07770.35780.01350.02240.29460.01630.3829-8.682327.3418-3.9666
42.074-6.9586-7.41545.68075.48775.5557-0.3458-0.3464-0.0699-0.07220.02860.9178-0.5902-0.85460.34460.50820.0738-0.02360.5328-0.02060.6329-23.964240.0144-0.6442
54.2816-2.4552-2.57276.75063.92175.97940.2144-0.23050.5492-0.4088-0.00290.1251-0.98-0.014-0.26910.5385-0.056-0.02560.30530.00330.451-16.097642.3928-4.3704
69.4614-2.79594.18913.8049-4.14244.76580.30380.2947-1.5774-0.69850.46291.41461.7462-0.1842-0.68530.6326-0.1028-0.01140.36210.01860.5601-13.672622.8974-10.3235
79.2142-3.28480.07721.6147-0.44456.4323-0.0587-1.0054-0.18940.00680.32560.101-0.0066-0.1758-0.28350.5053-0.0010.00730.35640.01230.4266-0.980525.39292.9125
87.2188-6.7829-6.54938.88957.06966.10430.24290.3647-0.1091-0.0671-0.52450.24360.2419-0.19220.19230.48640.1109-0.0350.91780.00820.438722.304410.7957-19.4271
90.12940.5622-0.78812.4422-3.40124.70340.57390.0849-0.04230.1169-0.3218-2.31160.81461.45940.11150.65270.19740.25720.9617-0.24321.460725.16831.0183-29.1482
109.55910.3794-2.09352.64511.04893.0028-0.16150.6564-0.4141-0.24070.1704-0.20310.38840.00230.01980.4972-0.0440.02320.3569-0.06360.32251.183530.2063-26.8437
115.42411.3631-5.37814.4453-1.19125.5252-0.41851.092-0.6817-0.30010.34280.31110.2762-1.08820.23270.4727-0.1934-0.06810.6625-0.01740.4727-26.750429.0144-18.4548
123.63995.651-1.46878.7797-2.16316.41560.12310.68840.5403-0.59651.2351.29380.6051-2.1937-1.47610.77620.1929-0.12531.94870.16920.9236-41.462228.3894-11.659
139.8370.0776-3.69385.7445-1.92632.03-0.4402-0.71210.37210.72341.13451.08840.0559-1.4766-0.57040.51570.01390.1060.70870.13280.7472-35.780227.442-2.2764
147.2951.9274-5.67381.6377-1.7597.0292-0.16840.24880.0009-0.06880.15820.15980.0405-0.14670.02190.2974-0.0519-0.05590.32560.01020.3721-16.672636.1987-19.0379
158.74921.10560.18535.3530.22514.0919-0.16590.1106-1.06240.24880.1797-0.1450.61440.0702-0.02680.55740.04890.0690.3497-0.11880.34443.01526.9066-23.7126
166.00310.3123-0.82074.1413-4.47655.0256-0.15260.55520.1479-1.1407-0.6899-2.468-0.32991.58960.65210.9365-0.08940.28731.1965-0.20451.421224.80337.9621-35.4536
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 184:198)A184 - 198
2X-RAY DIFFRACTION2(chain A and resid 199:222)A199 - 222
3X-RAY DIFFRACTION3(chain A and resid 223:235)A223 - 235
4X-RAY DIFFRACTION4(chain A and resid 236:249)A236 - 249
5X-RAY DIFFRACTION5(chain A and resid 250:951)A250 - 951
6X-RAY DIFFRACTION6(chain A and resid 952:960)A952 - 960
7X-RAY DIFFRACTION7(chain A and resid 961:981)A961 - 981
8X-RAY DIFFRACTION8(chain A and resid 982:1011)A982 - 1011
9X-RAY DIFFRACTION9(chain B and resid 202:208)B202 - 208
10X-RAY DIFFRACTION10(chain B and resid 209:233)B209 - 233
11X-RAY DIFFRACTION11(chain B and resid 234:248)B234 - 248
12X-RAY DIFFRACTION12(chain B and resid 249:255)B249 - 255
13X-RAY DIFFRACTION13(chain B and resid 256:925)B256 - 925
14X-RAY DIFFRACTION14(chain B and resid 926:959)B926 - 959
15X-RAY DIFFRACTION15(chain B and resid 960:992)B960 - 992
16X-RAY DIFFRACTION16(chain B and resid 993:998)B993 - 998

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