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- PDB-1e69: SMC head domain from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 1.0E+69
TitleSMC head domain from Thermotoga maritima
ComponentsCHROMOSOME SEGREGATION SMC PROTEIN
KeywordsCHROMOSOME SEGREGATION / SMC / STRUCTURAL MAINTENANCE OF CHROMOSOMES / COILED COIL
Function / homology
Function and homology information


chromosome condensation / sister chromatid cohesion / chromosome segregation / chromosome / DNA replication / ATP hydrolysis activity / DNA binding / 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 nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase ...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 nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chromosome partition protein Smc
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.1 Å
AuthorsLowe, J. / Cordell, S.C. / van den Ent, F.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal Structure of the Smc Head Domain: An Abc ATPase with 900 Residues Antiparallel Coiled-Coil Inserted
Authors: Lowe, J. / Cordell, S.C. / van den Ent, F.
History
DepositionAug 9, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 24, 2018Group: Database references / Source and taxonomy / Category: citation_author / entity_src_gen
Item: _citation_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._citation_author.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

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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
E: CHROMOSOME SEGREGATION SMC PROTEIN
F: CHROMOSOME SEGREGATION SMC PROTEIN


Theoretical massNumber of molelcules
Total (without water)215,3526
Polymers215,3526
Non-polymers00
Water0
1
A: CHROMOSOME SEGREGATION SMC PROTEIN


Theoretical massNumber of molelcules
Total (without water)35,8921
Polymers35,8921
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CHROMOSOME SEGREGATION SMC PROTEIN


Theoretical massNumber of molelcules
Total (without water)35,8921
Polymers35,8921
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: CHROMOSOME SEGREGATION SMC PROTEIN


Theoretical massNumber of molelcules
Total (without water)35,8921
Polymers35,8921
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: CHROMOSOME SEGREGATION SMC PROTEIN


Theoretical massNumber of molelcules
Total (without water)35,8921
Polymers35,8921
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: CHROMOSOME SEGREGATION SMC PROTEIN


Theoretical massNumber of molelcules
Total (without water)35,8921
Polymers35,8921
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
F: CHROMOSOME SEGREGATION SMC PROTEIN


Theoretical massNumber of molelcules
Total (without water)35,8921
Polymers35,8921
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)134.000, 49.190, 233.880
Angle α, β, γ (deg.)90.00, 94.63, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.07994, -0.88803, -0.45278), (0.50426, -0.42785, 0.75011), (-0.85985, -0.16836, 0.482)29.02715, 45.15533, 64.92871
2given(-0.00407, 0.54245, -0.84008), (-0.85334, 0.43986, -0.27989), (-0.52134, 0.71573, 0.46468)-43.35989, 89.12164, 66.444
3given(0.99797, 0.01748, 0.06128), (-0.01336, 0.99767, -0.06692), (-0.0623, 0.06596, 0.99588)-76.75986, 28.27685, 115.01768
4given(-0.12248, -0.86395, -0.48846), (0.5623, -0.46596, 0.68316), (-0.81781, -0.19099, 0.54287)44.61278, 69.35014, 182.20685
5given(0.03757, 0.50866, -0.86015), (-0.87666, -0.39637, -0.27269), (-0.47964, 0.7643, 0.43103)-117.83833, 108.36778, 183.293
DetailsTHE FUSION OF THE N- AND C- TERMINAL DOMAINS. SO FORTHIS CONSTRUCT THE BIOLOGICAL UNIT IS MONOMER

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Components

#1: Protein
CHROMOSOME SEGREGATION SMC PROTEIN


Mass: 35891.992 Da / Num. of mol.: 6
Fragment: SMC FUSION OF THE N- AND C-TERMINAL GLOBULAR DOMAINS RESIDUES 1-152 AND 1023-1164
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Cellular location: CYTOSOL / Plasmid: PHIS17 / Cellular location (production host): CYTOSOL / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.66 Å3/Da / Density % sol: 66 %
Crystal growpH: 5.6 / Details: pH 5.60
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
30.1 Msodium citrate1reservoir
40.1 Mammonium sulfate1reservoir
522 %PEG60001reservoir
60.013 mMurea1reservoir
2reservoir solution1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.93, 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 2000
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.931
20.981
ReflectionResolution: 3.1→30 Å / Num. obs: 45940 / % possible obs: 97.3 % / Redundancy: 2.3 % / Biso Wilson estimate: 68 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 11.4
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 3 / % possible all: 97.3
Reflection
*PLUS
Rmerge(I) obs: 0.071

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNS1phasing
SnBphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 3.1→100 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.272 2561 5 %RANDOM
Rwork0.25 ---
obs0.25 51643 97.3 %-
Displacement parametersBiso mean: 74 Å2
Baniso -1Baniso -2Baniso -3
1--1.367 Å20 Å2-25.303 Å2
2---12.378 Å20 Å2
3---13.746 Å2
Refinement stepCycle: LAST / Resolution: 3.1→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12396 0 0 0 12396
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.395
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_it1.3171.5
X-RAY DIFFRACTIONc_mcangle_it1.6782
X-RAY DIFFRACTIONc_scbond_it2.3892
X-RAY DIFFRACTIONc_scangle_it2.8532.5
Refine LS restraints NCSNCS model details: RESTRAINTS / Rms dev position: 0.05 Å / Weight position: 0.05

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