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- PDB-1bkn: CRYSTAL STRUCTURE OF AN N-TERMINAL 40KD FRAGMENT OF E. COLI DNA M... -

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Basic information

Entry
Database: PDB / ID: 1bkn
TitleCRYSTAL STRUCTURE OF AN N-TERMINAL 40KD FRAGMENT OF E. COLI DNA MISMATCH REPAIR PROTEIN MUTL
ComponentsMUTL
KeywordsDNA REPAIR / ATPASE / DNA BINDING
Function / homology
Function and homology information


single-stranded DNA-dependent ATP-dependent DNA helicase complex / mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication / mismatch repair complex / regulation of DNA recombination / nucleotide-excision repair, DNA duplex unwinding / mismatched DNA binding / ATP-dependent DNA damage sensor activity / mismatch repair / ATP hydrolysis activity / DNA binding ...single-stranded DNA-dependent ATP-dependent DNA helicase complex / mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication / mismatch repair complex / regulation of DNA recombination / nucleotide-excision repair, DNA duplex unwinding / mismatched DNA binding / ATP-dependent DNA damage sensor activity / mismatch repair / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding
Similarity search - Function
DNA mismatch repair protein, MutL / MutL, C-terminal domain, regulatory subdomain / MutL C terminal dimerisation domain / MutL, C-terminal, dimerisation / MutL, C-terminal domain superfamily / MutL, C-terminal domain, dimerisation subdomain / MutL C terminal dimerisation domain / DNA mismatch repair protein family, N-terminal / DNA mismatch repair protein, S5 domain 2-like / DNA mismatch repair, conserved site ...DNA mismatch repair protein, MutL / MutL, C-terminal domain, regulatory subdomain / MutL C terminal dimerisation domain / MutL, C-terminal, dimerisation / MutL, C-terminal domain superfamily / MutL, C-terminal domain, dimerisation subdomain / MutL C terminal dimerisation domain / DNA mismatch repair protein family, N-terminal / DNA mismatch repair protein, S5 domain 2-like / DNA mismatch repair, conserved site / DNA mismatch repair protein MutL/Mlh/Pms / DNA mismatch repair protein, C-terminal domain / DNA mismatch repair proteins mutL / hexB / PMS1 signature. / DNA mismatch repair protein, C-terminal domain / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA mismatch repair protein MutL
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.9 Å
AuthorsYang, W. / Ban, C.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1998
Title: Crystal structure and ATPase activity of MutL: implications for DNA repair and mutagenesis.
Authors: Ban, C. / Yang, W.
History
DepositionJul 9, 1998Processing site: BNL
Revision 1.0May 11, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MUTL
B: MUTL


Theoretical massNumber of molelcules
Total (without water)78,5992
Polymers78,5992
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.200, 93.200, 221.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.041784, 0.989309, -0.139721), (0.999101, -0.040365, 0.012974), (0.007196, -0.140137, -0.990106)
Vector: 68.73042, -63.03986, 173.24435)

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Components

#1: Protein MUTL


Mass: 39299.602 Da / Num. of mol.: 2 / Fragment: N-TERMINAL 40KD FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: MUTL / Plasmid: PTX418 / Gene (production host): MUTL / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 (LAMBDA DE3) / References: UniProt: P23367
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST THREE RESIDUES IN THE SEQUENCE ARE NOT ENCODED BY E. COLI MUTL GENE. THEY ARE FUSED INTO ...THE FIRST THREE RESIDUES IN THE SEQUENCE ARE NOT ENCODED BY E. COLI MUTL GENE. THEY ARE FUSED INTO MUTL PROTEIN DUE TO CLONING AND EXPRESSION.

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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: 2.86 Å3/Da / Density % sol: 57 %
Description: DATA TO 2.9A ARE USED FOR THE STRUCTURE REFINEMENT. THE LAST SHELL (2.9A TO 3.0A) HAS RSYM OF 0.50, COMPLETENESS OF 98.3% AND I/SIGI OF 2.1.
Crystal growpH: 6.6 / Details: pH 6.6
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMbis-Tris propane1reservoir
2100 mMmagnesium acetate1reservoir
3100 mMmagnesium sulfate1reservoir
42 mMdithiothreitol1reservoir
520 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Aug 1, 1997 / Details: MIRROR
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 23519 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 84.7 Å2 / Rsym value: 0.074 / Net I/σ(I): 8.3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.1 / Rsym value: 0.7 / % possible all: 84.6
Reflection
*PLUS
Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 84.6 % / Rmerge(I) obs: 0.696

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Processing

Software
NameVersionClassification
MAMAmodel building
X-PLOR3.851refinement
HKLdata reduction
CCP4data scaling
MAMAphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.9→20 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.3 963 4.8 %RANDOM
Rwork0.248 ---
obs0.248 19961 98 %-
Displacement parametersBiso mean: 73.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.73 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4237 0 0 165 4402
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg0.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.49
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.531.5
X-RAY DIFFRACTIONx_mcangle_it5.792
X-RAY DIFFRACTIONx_scbond_it5.772
X-RAY DIFFRACTIONx_scangle_it8.782.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.388 151 4.6 %
Rwork0.362 3117 -
obs--98.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1TOPPAR:PROTEIN_REP.PARAMTOPPAR:TOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.3
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.49

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