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- PDB-3zgx: Crystal structure of the kleisin-N SMC interface in prokaryotic c... -

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Basic information

Entry
Database: PDB / ID: 3zgx
TitleCrystal structure of the kleisin-N SMC interface in prokaryotic condensin
Components
  • CHROMOSOME PARTITION PROTEIN SMC
  • SEGREGATION AND CONDENSATION PROTEIN A
KeywordsCELL CYCLE
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
Helix Hairpins - #1720 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2410 / 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 ...Helix Hairpins - #1720 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2410 / 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 / Helix Hairpins / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Segregation and condensation protein A / Chromosome partition protein Smc
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.4 Å
AuthorsBurmann, F. / Shin, H. / Basquin, J. / Soh, Y. / Gimenez, V. / Kim, Y. / Oh, B. / Gruber, S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: An Asymmetric Smc-Kleisin Bridge in Prokaryotic Condensin.
Authors: Burmann, F. / Shin, H. / Basquin, J. / Soh, Y. / Gimenez-Oya, V. / Kim, Y. / Oh, B. / Gruber, S.
History
DepositionDec 19, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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
Z: SEGREGATION AND CONDENSATION PROTEIN A


Theoretical massNumber of molelcules
Total (without water)118,6994
Polymers118,6994
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10400 Å2
ΔGint-84 kcal/mol
Surface area40010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.435, 107.435, 102.821
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN B AND (RESSEQ 1:32 OR RESSEQ 36:52 OR RESSEQ...
211CHAIN A AND (RESSEQ 1:32 OR RESSEQ 36:52 OR RESSEQ...
112CHAIN Z AND (RESSEQ 10:76 )
212CHAIN C AND (RESSEQ 10:76 )

NCS ensembles :
ID
1
2

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Components

#1: Protein CHROMOSOME PARTITION PROTEIN SMC / SMC


Mass: 48166.711 Da / Num. of mol.: 2 / Fragment: SMC HEAD DOMAIN, RESIDUES 1-219,983-1186
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: 1A700 / Plasmid: PET28 POLYCISTRONIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): GOLD / References: UniProt: P51834
#2: Protein SEGREGATION AND CONDENSATION PROTEIN A / KLEISIN


Mass: 11182.849 Da / Num. of mol.: 2 / Fragment: N TERMINAL DOMAIN OF SCPA, RESIDUES 1-86
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: 1A700 / Plasmid: PET 28 POLYCISTRONIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): GOLD / References: UniProt: P35154
Sequence detailsC TERMINAL HEXAHISTIDINE TAG

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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: 2.54 Å3/Da / Density % sol: 51.5 % / Description: NONE
Crystal growpH: 6.5
Details: 8 % ISOPROPANOL, 20 MM MAGNESIUM CHLORIDE AND 50 MM MES PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9793
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.49
ReflectionResolution: 3.4→75.97 Å / Num. obs: 16156 / % possible obs: 99.9 % / Observed criterion σ(I): 3.3 / Redundancy: 9.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.8
Reflection shellResolution: 3.4→3.58 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.3 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3.4→75.968 Å / σ(F): 1.99 / Phase error: 33.28 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.277 1581 5 %
Rwork0.243 --
obs0.2418 16156 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→75.968 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6349 0 0 0 6349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016432
X-RAY DIFFRACTIONf_angle_d1.5738696
X-RAY DIFFRACTIONf_dihedral_angle_d19.4392326
X-RAY DIFFRACTIONf_chiral_restr0.111038
X-RAY DIFFRACTIONf_plane_restr0.0061119
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B2609X-RAY DIFFRACTIONPOSITIONAL
12A2609X-RAY DIFFRACTIONPOSITIONAL0.021
21Z534X-RAY DIFFRACTIONPOSITIONAL
22C534X-RAY DIFFRACTIONPOSITIONAL0.029
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.402-3.51180.31461420.3022661X-RAY DIFFRACTION93
3.5118-3.63730.30161430.28992729X-RAY DIFFRACTION95
3.6373-3.78290.32391440.28052719X-RAY DIFFRACTION95
3.7829-3.95510.36631450.2692731X-RAY DIFFRACTION95
3.9551-4.16360.29141430.26232730X-RAY DIFFRACTION95
4.1636-4.42440.26871440.24692707X-RAY DIFFRACTION95
4.4244-4.7660.27451440.21972746X-RAY DIFFRACTION95
4.766-5.24550.23261450.21682698X-RAY DIFFRACTION95
5.2455-6.00430.32611450.24522738X-RAY DIFFRACTION95
6.0043-7.56360.32821440.25952719X-RAY DIFFRACTION95
7.5636-74.30070.21261400.20242736X-RAY DIFFRACTION95

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