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- PDB-3htk: Crystal structure of Mms21 and Smc5 complex -

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Basic information

Entry
Database: PDB / ID: 3htk
TitleCrystal structure of Mms21 and Smc5 complex
Components
  • (Structural maintenance of chromosomes protein 5) x 2
  • E3 SUMO-protein ligase MMS21
KeywordsRECOMBINATION/REPLICATION/LIGASE / SUMO E3 ligase / SPL-RING / RING / ATP-binding / Chromosomal protein / Coiled coil / DNA damage / DNA recombination / DNA repair / Nucleotide-binding / Nucleus / Ubl conjugation / Cytoplasm / Ligase / Metal-binding / Ubl conjugation pathway / Zinc / Zinc-finger / RECOMBINATION-REPLICATION-LIGASE COMPLEX
Function / homology
Function and homology information


Smc5-Smc6 complex / resolution of DNA recombination intermediates / DNA double-strand break attachment to nuclear envelope / chromosome separation / SUMO ligase activity / SUMOylation of DNA damage response and repair proteins / chromatin looping / protein serine/threonine kinase inhibitor activity / Transferases; Acyltransferases; Aminoacyltransferases / recombinational repair ...Smc5-Smc6 complex / resolution of DNA recombination intermediates / DNA double-strand break attachment to nuclear envelope / chromosome separation / SUMO ligase activity / SUMOylation of DNA damage response and repair proteins / chromatin looping / protein serine/threonine kinase inhibitor activity / Transferases; Acyltransferases; Aminoacyltransferases / recombinational repair / regulation of telomere maintenance / SUMO transferase activity / protein sumoylation / double-strand break repair via homologous recombination / single-stranded DNA binding / nuclear envelope / damaged DNA binding / chromosome, telomeric region / DNA repair / ATP hydrolysis activity / zinc ion binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1010 / E3 SUMO-protein ligase Nse2 (Mms21) / Zinc-finger of the MIZ type in Nse subunit / Structural maintenance of chromosomes protein 5 / Zinc finger, MIZ-type / Zinc finger SP-RING-type profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1010 / E3 SUMO-protein ligase Nse2 (Mms21) / Zinc-finger of the MIZ type in Nse subunit / Structural maintenance of chromosomes protein 5 / Zinc finger, MIZ-type / Zinc finger SP-RING-type profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
E3 SUMO-protein ligase MMS21 / Structural maintenance of chromosomes protein 5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.31 Å
AuthorsDuan, X. / Sarangi, P. / Liu, X. / Rangi, G.K. / Zhao, X. / Ye, H.
CitationJournal: Mol.Cell / Year: 2009
Title: Structural and functional insights into the roles of the Mms21 subunit of the Smc5/6 complex.
Authors: Duan, X. / Sarangi, P. / Liu, X. / Rangi, G.K. / Zhao, X. / Ye, H.
History
DepositionJun 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Structural maintenance of chromosomes protein 5
B: Structural maintenance of chromosomes protein 5
C: E3 SUMO-protein ligase MMS21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1994
Polymers46,1333
Non-polymers651
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-69 kcal/mol
Surface area22090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.465, 91.574, 249.215
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Structural maintenance of chromosomes protein 5


Mass: 7264.308 Da / Num. of mol.: 1 / Fragment: N-terminal coil
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SMC5, YOL034W / Plasmid: pET24D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q08204
#2: Protein Structural maintenance of chromosomes protein 5


Mass: 8480.769 Da / Num. of mol.: 1 / Fragment: C-terminal coil
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SMC5, YOL034W / Plasmid: pET24D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q08204
#3: Protein E3 SUMO-protein ligase MMS21 / Methyl methanesulfonate-sensitivity protein 21 / Non-structural maintenance of chromosome element 2 ...Methyl methanesulfonate-sensitivity protein 21 / Non-structural maintenance of chromosome element 2 / Non-SMC element 2


Mass: 30388.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MMS21, NSE2, YEL019C / Plasmid: pET24D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P38632, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.94 Å3/Da / Density % sol: 58.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 18% PEG 3350, 40mM CaCl2, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.97899
SYNCHROTRONAPS 24-ID-C20.97916
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDNov 4, 2006
ADSC QUANTUM 3152CCDMay 17, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.978991
20.979161
ReflectionResolution: 2.3→50 Å / Num. obs: 21519 / % possible obs: 88 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Rmerge(I) obs: 0.09
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.6 / % possible all: 77.3

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.31→50 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.912 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.464 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1038 5.2 %RANDOM
Rwork0.256 ---
obs0.257 20105 81.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 195.71 Å2 / Biso mean: 59.597 Å2 / Biso min: 8.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20 Å20 Å2
2--0.52 Å20 Å2
3----1.21 Å2
Refinement stepCycle: LAST / Resolution: 2.31→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3104 0 1 117 3222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223155
X-RAY DIFFRACTIONr_angle_refined_deg1.2661.9784261
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6745384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.08926.424151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.14215612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6111511
X-RAY DIFFRACTIONr_chiral_restr0.0910.2482
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022348
X-RAY DIFFRACTIONr_nbd_refined0.2890.21723
X-RAY DIFFRACTIONr_nbtor_refined0.3220.22283
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2120
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2810.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.22
X-RAY DIFFRACTIONr_mcbond_it12.7491.51946
X-RAY DIFFRACTIONr_mcangle_it17.31723173
X-RAY DIFFRACTIONr_scbond_it5.35331209
X-RAY DIFFRACTIONr_scangle_it8.0264.51088
LS refinement shellResolution: 2.306→2.366 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 51 -
Rwork0.387 784 -
all-835 -
obs--46.21 %

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