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- PDB-4och: Apo structure of Smr domain of MutS2 from Deinococcus radiodurans -

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Basic information

Entry
Database: PDB / ID: 4och
TitleApo structure of Smr domain of MutS2 from Deinococcus radiodurans
ComponentsEndonuclease MutS2
KeywordsHYDROLASE / nuclease / Mn2+ ion
Function / homology
Function and homology information


mismatched DNA binding / negative regulation of DNA recombination / ATP-dependent DNA damage sensor activity / mismatch repair / double-stranded DNA binding / endonuclease activity / Hydrolases; Acting on ester bonds / ATP hydrolysis activity / ATP binding
Similarity search - Function
Ribosomal Protein S8; Chain: A, domain 1 - #110 / MutS2 and Smr-associated SH3 domain / MutS2 and Smr-associated SH3 domain / Endonuclease MutS2 / Smr domain superfamily / Smr domain / Small MutS-related domain / Smr domain / Smr domain profile. / DNA mismatch repair MutS family ...Ribosomal Protein S8; Chain: A, domain 1 - #110 / MutS2 and Smr-associated SH3 domain / MutS2 and Smr-associated SH3 domain / Endonuclease MutS2 / Smr domain superfamily / Smr domain / Small MutS-related domain / Smr domain / Smr domain profile. / DNA mismatch repair MutS family / DNA mismatch repair protein MutS, C-terminal / DNA mismatch repair protein MutS, core / DNA mismatch repair protein MutS, core domain superfamily / MutS domain V / DNA mismatch repair proteins mutS family signature. / DNA-binding domain of DNA mismatch repair MUTS family / ATPase domain of DNA mismatch repair MUTS family / Ribosomal Protein S8; Chain: A, domain 1 / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4001 Å
AuthorsZhang, H. / Zhao, Y. / Xu, Q. / Hua, Y.J.
CitationJournal: Dna Repair / Year: 2014
Title: Structural and functional studies of MutS2 from Deinococcus radiodurans.
Authors: Zhang, H. / Xu, Q. / Lu, M. / Xu, X. / Wang, Y. / Wang, L. / Zhao, Y. / Hua, Y.
History
DepositionJan 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Endonuclease MutS2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9572
Polymers9,8651
Non-polymers921
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)24.980, 47.510, 30.810
Angle α, β, γ (deg.)90.00, 99.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Endonuclease MutS2


Mass: 9865.203 Da / Num. of mol.: 1 / Fragment: Smr domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: mutS2, DR_1976 / Production host: Escherichia coli (E. coli) / Strain (production host): BL(21)DE3
References: UniProt: Q9RSZ3, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 1.83 Å3/Da / Density % sol: 32.7 %
Crystal growTemperature: 297 K
Method: crystal formed spontaneously in protein solution stored at 4 degree
pH: 8.8
Details: 30mM NaCl and 20mM Tris-HCl, pH 8.8, crystal formed spontaneously in protein solution stored at 4 degree, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 2, 2011
RadiationMonochromator: silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. all: 14061 / Num. obs: 13788 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.02
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.4-1.443.70.72.39197.8
1.44-1.48197.8
1.48-1.52198.4
1.52-1.57198.6
1.57-1.62198.7
1.62-1.67199.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4001→25.598 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 24.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2206 681 4.94 %
Rwork0.1923 --
obs0.1937 13778 98.04 %
all-14053 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4001→25.598 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms641 0 6 109 756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015674
X-RAY DIFFRACTIONf_angle_d1.776904
X-RAY DIFFRACTIONf_dihedral_angle_d14.821263
X-RAY DIFFRACTIONf_chiral_restr0.108101
X-RAY DIFFRACTIONf_plane_restr0.009120
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4001-1.50810.31591220.25112590X-RAY DIFFRACTION98
1.5081-1.65990.21891410.1752642X-RAY DIFFRACTION99
1.6599-1.90.21991500.17632613X-RAY DIFFRACTION99
1.9-2.39350.24971390.22352545X-RAY DIFFRACTION96
2.3935-25.60230.18371290.17052707X-RAY DIFFRACTION99

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