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- PDB-4u4p: Crystal structure of the human condensin SMC hinge domain heterod... -

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Basic information

Entry
Database: PDB / ID: 4u4p
TitleCrystal structure of the human condensin SMC hinge domain heterodimer with short coiled coils
Components
  • Structural maintenance of chromosomes protein 2
  • Structural maintenance of chromosomes protein 4
KeywordsPROTEIN BINDING / Condensin / SMC
Function / homology
Function and homology information


condensin complex => GO:0000796 / condensin complex => GO:0000796 / meiotic chromosome condensation / condensin complex / kinetochore organization / meiotic chromosome segregation / mitotic chromosome condensation / Condensation of Prometaphase Chromosomes / nuclear chromosome / mitotic sister chromatid segregation ...condensin complex => GO:0000796 / condensin complex => GO:0000796 / meiotic chromosome condensation / condensin complex / kinetochore organization / meiotic chromosome segregation / mitotic chromosome condensation / Condensation of Prometaphase Chromosomes / nuclear chromosome / mitotic sister chromatid segregation / chromosome, centromeric region / condensed chromosome / Condensation of Prophase Chromosomes / single-stranded DNA binding / nuclear speck / cell division / nucleolus / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Structural maintenance of chromosomes 4, ABC domain, eukaryotic / Smc2, ATP-binding cassette domain / 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
Structural maintenance of chromosomes protein 2 / Structural maintenance of chromosomes protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å
AuthorsUchiyama, S. / Kawahara, K. / Hosokawa, Y. / Fukakusa, S. / Oki, H. / Nakamura, S. / Noda, M. / Takino, R. / Miyahara, Y. / Maruno, T. ...Uchiyama, S. / Kawahara, K. / Hosokawa, Y. / Fukakusa, S. / Oki, H. / Nakamura, S. / Noda, M. / Takino, R. / Miyahara, Y. / Maruno, T. / Kobayashi, Y. / Ohkubo, T. / Fukui, K.
CitationJournal: to be published
Title: Structural basis for dimer information and DNA recognition of human SMC proteins
Authors: Uchiyama, S. / Kawahara, K. / Hosokawa, Y. / Fukakusa, S. / Oki, H. / Nakamura, S. / Noda, M. / Takino, R. / Miyahara, Y. / Maruno, T. / Kobayashi, Y. / Ohkubo, T. / Fukui, K.
History
DepositionJul 24, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Structural maintenance of chromosomes protein 2
B: Structural maintenance of chromosomes protein 4


Theoretical massNumber of molelcules
Total (without water)54,1842
Polymers54,1842
Non-polymers00
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-16 kcal/mol
Surface area21390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.400, 93.980, 102.070
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 Structural maintenance of chromosomes protein 2 / SMC-2 / Chromosome-associated protein E / hCAP-E / XCAP-E homolog


Mass: 26278.309 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 476-707
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMC2, CAPE, SMC2L1, PRO0324 / Production host: Escherichia coli (E. coli) / References: UniProt: O95347
#2: Protein Structural maintenance of chromosomes protein 4 / SMC-4 / Chromosome-associated polypeptide C / hCAP-C / XCAP-C homolog


Mass: 27906.041 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 566-809
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMC4, CAPC, SMC4L1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NTJ3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.23 Å3/Da / Density % sol: 44.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris-HCl pH 8.5, 19% PEG 3350, 50mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.89→46.99 Å / Num. obs: 47639 / % possible obs: 98.4 % / Redundancy: 4.4 % / Biso Wilson estimate: 23.43 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.044 / Net I/σ(I): 10.8 / Num. measured all: 209398 / Scaling rejects: 29
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.89-1.934.30.4762.6876726570.3650.63799.5
8.99-46.993.90.04126.915133890.9960.02491.1

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Phasing

PhasingMethod: molecular replacement

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Processing

SoftwareName: PHENIX / Version: 1.9_1692 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L51

3l51


Resolution: 1.89→45.191 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / Phase error: 22.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2347 1930 4.99 %Random selection
Rwork0.1878 ---
obs0.19 38707 97.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.89→45.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3372 0 0 303 3675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073415
X-RAY DIFFRACTIONf_angle_d0.9744592
X-RAY DIFFRACTIONf_dihedral_angle_d14.5071313
X-RAY DIFFRACTIONf_chiral_restr0.041529
X-RAY DIFFRACTIONf_plane_restr0.004589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.93730.28891370.26032627X-RAY DIFFRACTION99
1.9373-1.98960.2591350.2372605X-RAY DIFFRACTION99
1.9896-2.04820.26831500.22092620X-RAY DIFFRACTION99
2.0482-2.11430.26431340.20032625X-RAY DIFFRACTION99
2.1143-2.18990.2491410.19592626X-RAY DIFFRACTION99
2.1899-2.27750.24991370.19262625X-RAY DIFFRACTION99
2.2775-2.38120.27841410.19462617X-RAY DIFFRACTION98
2.3812-2.50670.24651350.19232620X-RAY DIFFRACTION99
2.5067-2.66380.24431310.20192657X-RAY DIFFRACTION98
2.6638-2.86940.28281370.19672618X-RAY DIFFRACTION98
2.8694-3.15810.21281430.18442641X-RAY DIFFRACTION98
3.1581-3.61490.22421280.16822645X-RAY DIFFRACTION97
3.6149-4.55370.1881410.15582593X-RAY DIFFRACTION95
4.5537-45.20390.22491400.19022658X-RAY DIFFRACTION92

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