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- PDB-1gxl: SMC hinge domain from T. maritima with coiled coil -

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Basic information

Entry
Database: PDB / ID: 1gxl
TitleSMC hinge domain from T. maritima with coiled coil
ComponentsCHROMOSOME SEGREGATION SMC PROTEIN
KeywordsCHROMOSOME SEGREGATION / SMC DIMERISATION DOMAIN / ANTI PARALLEL COILED COIL / SMC PROTEINS
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
Taq DNA Polymerase; Chain T, domain 4 - #20 / Alpha-Beta Plaits - #1620 / 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 ...Taq DNA Polymerase; Chain T, domain 4 - #20 / Alpha-Beta Plaits - #1620 / 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 / Taq DNA Polymerase; Chain T, domain 4 / Alpha-Beta Plaits / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chromosome partition protein Smc
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLowe, J. / Haering, C. / Nasmyth, K.
CitationJournal: Mol.Cell / Year: 2002
Title: Molecular Architecture of Smc Proteins and the Yeast Cohesin Complex
Authors: Haering, C. / Lowe, J. / Hochwagen, A. / Nasmyth, K.
History
DepositionApr 7, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jan 24, 2018Group: Atomic model / Source and taxonomy / Category: atom_site / entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 2.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
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

Downloads & links

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Assembly

Deposited unit
A: CHROMOSOME SEGREGATION SMC PROTEIN
B: CHROMOSOME SEGREGATION SMC PROTEIN
C: CHROMOSOME SEGREGATION SMC PROTEIN
D: CHROMOSOME SEGREGATION SMC PROTEIN


Theoretical massNumber of molelcules
Total (without water)97,0474
Polymers97,0474
Non-polymers00
Water00
1
A: CHROMOSOME SEGREGATION SMC PROTEIN
B: CHROMOSOME SEGREGATION SMC PROTEIN


Theoretical massNumber of molelcules
Total (without water)48,5232
Polymers48,5232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: CHROMOSOME SEGREGATION SMC PROTEIN
D: CHROMOSOME SEGREGATION SMC PROTEIN


Theoretical massNumber of molelcules
Total (without water)48,5232
Polymers48,5232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)136.400, 115.500, 68.960
Angle α, β, γ (deg.)90.00, 93.70, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
CHROMOSOME SEGREGATION SMC PROTEIN / SMC


Mass: 24261.680 Da / Num. of mol.: 4 / Fragment: HINGE DOMAIN RESIDUES 473-685
Source method: isolated from a genetically manipulated source
Details: HINGE DOMAIN FROM T. MARITIMA, RESIDUES 473-685 / Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Strain: DSMZ 3109 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q9X0R4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 60 %
Crystal growpH: 4.6 / Details: pH 4.60
Crystal grow
*PLUS
Temperature: 19 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Msodium citrate1reservoir
20.1 Msodium cacodylate1reservoir
330 %iso-propanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9793
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 18320 / % possible obs: 95.1 % / Redundancy: 5.1 % / Biso Wilson estimate: 110.1 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 16.3
Reflection shellResolution: 3→3.16 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 2.9 / % possible all: 92.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: P212121 CRYSTAL FORM

Resolution: 3→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.301 1023 5 %RANDOM
Rwork0.2524 ---
obs0.2524 20309 94.8 %-
Displacement parametersBiso mean: 84.97 Å2
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6490 0 0 0 6490
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.363
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINT / Rms dev position: 0.23 Å / Weight position: 100
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.252 / Rfactor Rwork: 0.252
Solvent computation
*PLUS
Displacement parameters
*PLUS

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