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- PDB-2aoq: Crystal structure of MutH-unmethylated DNA complex -

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Basic information

Entry
Database: PDB / ID: 2aoq
TitleCrystal structure of MutH-unmethylated DNA complex
Components
  • 5'-D(*GP*CP*AP*TP*GP*AP*TP*CP*AP*TP*GP*C)-3'
  • DNA mismatch repair protein mutH
KeywordsHydrolase/DNA / GATC recognition / Hydrolase-DNA COMPLEX
Function / homology
Function and homology information


DNA modification / mismatch repair / endonuclease activity / DNA binding / cytoplasm
Similarity search - Function
DNA mismatch repair protein MutH / DNA mismatch repair MutH/Type II restriction enzyme Sau3AI / DNA mismatch repair enzyme MutH / DNA mismatch repair enzyme MutH / DNA mismatch repair MutH/Restriction endonuclease, type II / DNA mismatch repair MutH/Type II restriction endonuclease superfamily / ECO RV Endonuclease; Chain A / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA mismatch repair protein MutH
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLee, J.Y. / Chang, J. / Joseph, N. / Ghirlando, R. / Rao, D.N. / Yang, W.
CitationJournal: Mol.Cell / Year: 2005
Title: MutH complexed with hemi- and unmethylated DNAs: coupling base recognition and DNA cleavage.
Authors: Lee, J.Y. / Chang, J. / Joseph, N. / Ghirlando, R. / Rao, D.N. / Yang, W.
History
DepositionAug 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
B: 5'-D(*GP*CP*AP*TP*GP*AP*TP*CP*AP*TP*GP*C)-3'
C: 5'-D(*GP*CP*AP*TP*GP*AP*TP*CP*AP*TP*GP*C)-3'
A: DNA mismatch repair protein mutH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3425
Polymers32,2623
Non-polymers802
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.624, 114.624, 46.755
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: DNA chain 5'-D(*GP*CP*AP*TP*GP*AP*TP*CP*AP*TP*GP*C)-3'


Mass: 3662.404 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein DNA mismatch repair protein mutH / Methyl-directed mismatch repair protein


Mass: 24936.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: mutH / Plasmid: pET15b-MutH / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P44688
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, calcium acetate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2calcium acetate11
3cacodylate11
4H2O11
5PEG 800012
6calcium acetate12
7cacodylate12
8H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 25, 2004
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 17994 / Num. obs: 16986 / % possible obs: 94.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.4 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 30.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 1.65 / Num. unique all: 1148 / % possible all: 64.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AZO, chain B

2azo


Resolution: 2.2→19.85 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 428123.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1642 10 %RANDOM
Rwork0.199 ---
obs0.199 16344 90.8 %-
all-18030 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.7681 Å2 / ksol: 0.361596 e/Å3
Displacement parametersBiso mean: 49.5 Å2
Baniso -1Baniso -2Baniso -3
1-6.56 Å28.96 Å20 Å2
2--6.56 Å20 Å2
3----13.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1710 486 2 154 2352
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d1.08
X-RAY DIFFRACTIONc_mcbond_it1.51.5
X-RAY DIFFRACTIONc_mcangle_it2.62
X-RAY DIFFRACTIONc_scbond_it2.142
X-RAY DIFFRACTIONc_scangle_it3.312.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.37 177 9.7 %
Rwork0.322 1654 -
obs--61.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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