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- PDB-5xg3: Crystal structure of the ATPgS-engaged Smc head domain with an ex... -

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Basic information

Entry
Database: PDB / ID: 5xg3
TitleCrystal structure of the ATPgS-engaged Smc head domain with an extended coiled coil bound to the C-terminal domain of ScpA derived from Bacillus subtilis
Components
  • Chromosome partition protein Smc
  • Segregation and condensation protein A
KeywordsDNA BINDING PROTEIN/CELL CYCLE / Condensin / Smc / ATPase / ScpA / DNA BINDING PROTEIN-CELL CYCLE complex
Function / homology
Function and homology information


chromosome condensation / sister chromatid cohesion / chromosome segregation / chromosome / DNA replication / cell division / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Segregation and condensation protein A / Segregation and condensation protein ScpA / Structural maintenance of chromosomes protein, prokaryotic / ScpA-like, C-terminal / 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 ...Segregation and condensation protein A / Segregation and condensation protein ScpA / Structural maintenance of chromosomes protein, prokaryotic / ScpA-like, C-terminal / 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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / : / : / Segregation and condensation protein A / Chromosome partition protein Smc
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsShin, H.-C. / Lee, H. / Oh, B.-H.
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 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromosome partition protein Smc
B: Chromosome partition protein Smc
C: Segregation and condensation protein A
D: Segregation and condensation protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,1989
Polymers119,0444
Non-polymers1,1545
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7690 Å2
ΔGint-64 kcal/mol
Surface area41470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.103, 104.783, 185.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Chromosome partition protein Smc


Mass: 49153.883 Da / Num. of mol.: 2 / Fragment: UNP residues 1-219,UNP residues 975-1186 / Mutation: E1118Q,E1118Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: smc, ylqA, BSU15940 / Production host: Escherichia coli (E. coli) / References: UniProt: P51834
#2: Protein Segregation and condensation protein A


Mass: 10367.890 Da / Num. of mol.: 2 / Fragment: UNP residues 167-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: scpA, SAMN05878487_2386 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1N6WAJ8, UniProt: P35154*PLUS

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Non-polymers , 4 types, 8 molecules

#3: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.59 Å3/Da / Density % sol: 65.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% PEG 3000, 0.1M Imidazole pH8.0, 0.2M LiSO4, 0.05M Hexamine cobalt (III) chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 35074 / % possible obs: 92.6 % / Redundancy: 5.4 % / Biso Wilson estimate: 57.51 Å2 / Net I/σ(I): 12.3

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXphasing
HKLdata reduction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XEX

1xex


Resolution: 3.5→40.989 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.7 / Phase error: 27.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2956 2393 6.82 %
Rwork0.2607 32681 -
obs0.2631 35074 84.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.68 Å2 / Biso mean: 54.4176 Å2 / Biso min: 3.91 Å2
Refinement stepCycle: final / Resolution: 3.5→40.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5637 0 65 3 5705
Biso mean--43.72 26.18 -
Num. residues----866
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015751
X-RAY DIFFRACTIONf_angle_d1.3127874
X-RAY DIFFRACTIONf_chiral_restr0.061007
X-RAY DIFFRACTIONf_plane_restr0.0091034
X-RAY DIFFRACTIONf_dihedral_angle_d11.3563382
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5001-3.57150.33671100.31141579168970
3.5715-3.64910.39731270.30011728185575
3.6491-3.73390.28831350.28751855199080
3.7339-3.82730.28991370.2711794193179
3.8273-3.93070.36171280.27081727185576
3.9307-4.04620.27411280.261712184074
4.0462-4.17670.31221220.23911755187776
4.1767-4.32580.29071380.23641876201483
4.3258-4.49880.23971470.22982040218790
4.4988-4.70330.24841450.24061989213486
4.7033-4.95090.30521490.23892003215288
4.9509-5.26050.31861540.25712026218088
5.2605-5.66570.30821460.28581995214188
5.6657-6.2340.351540.29282075222989
6.234-7.1320.30731470.28552070221791
7.132-8.97010.28911620.24332205236796
8.9701-40.99140.24771640.24682252241699

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