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- PDB-1gxk: SMC hinge domain from T. maritima w/o coiled coil, P212121 crysta... -

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Basic information

Entry
Database: PDB / ID: 1gxk
TitleSMC hinge domain from T. maritima w/o coiled coil, P212121 crystal form
ComponentsCHROMOSOME SEGREGATION SMC PROTEIN
KeywordsCHROMOSOME SEGREGATION / SMC DIMERISATION DOMAIN / ANTI PARALLEL COILED COIL / SMC PROTEINS / COMPLETE PROTEOME.
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
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 1.3Jan 24, 2018Group: Source and taxonomy / Category: 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 1.4Dec 13, 2023Group: 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)83,3794
Polymers83,3794
Non-polymers00
Water00
1
A: CHROMOSOME SEGREGATION SMC PROTEIN
B: CHROMOSOME SEGREGATION SMC PROTEIN


Theoretical massNumber of molelcules
Total (without water)41,6902
Polymers41,6902
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)41,6902
Polymers41,6902
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)58.900, 62.210, 225.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
CHROMOSOME SEGREGATION SMC PROTEIN / SMC


Mass: 20844.791 Da / Num. of mol.: 4 / Fragment: HINGE DOMAIN RESIDUES 485-670
Source method: isolated from a genetically manipulated source
Details: HINGE DOMAIN FROM T. MARITIMA, RESIDUES 485-670, ORTHORHOMBIC FORM
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: 2.47 Å3/Da / Density % sol: 45 %
Crystal growpH: 9.2 / Details: pH 9.20
Crystal grow
*PLUS
Temperature: 19 ℃ / Method: vapor diffusion, sitting drop / pH: 6.9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 %PEG2000 MME1reservoir
20.1 MTris1reservoirpH6.9
310 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.93
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 13536 / % possible obs: 92.7 % / Redundancy: 2.8 % / Biso Wilson estimate: 44 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 10.6
Reflection shellResolution: 3→3.16 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 3.1 / % 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: P21 CRYSTAL FORM, PDB ID 1GXJ

1gxj


Resolution: 3→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: DATA IS TWINNED. TWIN OPERATOR K, H, - TWIN FRACTION 0.158
RfactorNum. reflection% reflectionSelection details
Rfree0.2984 709 5 %TWIN RELATED
Rwork0.2528 ---
obs0.2528 14473 83.5 %-
Displacement parametersBiso mean: 49.68 Å2
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4867 0 0 0 4867
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_deg1.332
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: 0.1084 Å / Weight position: 300
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.253 / Rfactor Rfree: 0.298 / Rfactor Rwork: 0.253
Solvent computation
*PLUS
Displacement parameters
*PLUS

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