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- PDB-1nhi: Crystal structure of N-terminal 40KD MutL (LN40) complex with ADP... -

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Basic information

Entry
Database: PDB / ID: 1nhi
TitleCrystal structure of N-terminal 40KD MutL (LN40) complex with ADPnP and one potassium
ComponentsDNA mismatch repair protein mutL
KeywordsREPLICATION / SIGNALING PROTEIN / DNA mismatch repair / MutL / ATPase / Rubidium
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 / 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-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / DNA mismatch repair protein MutL / DNA mismatch repair protein MutL
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHu, X. / Machius, M. / Yang, W.
CitationJournal: FEBS Lett. / Year: 2003
Title: Monovalent cation dependence and preference of GHKL ATPases and kinases
Authors: Hu, X. / Machius, M. / Yang, W.
History
DepositionDec 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 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_ref_seq_dif / 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_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_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_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_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_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

Downloads & links

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Assembly

Deposited unit
A: DNA mismatch repair protein mutL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9096
Polymers37,2151
Non-polymers6945
Water3,315184
1
A: DNA mismatch repair protein mutL
hetero molecules

A: DNA mismatch repair protein mutL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,81812
Polymers74,4312
Non-polymers1,38710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area7730 Å2
ΔGint-42 kcal/mol
Surface area28610 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)61.897, 71.415, 190.342
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Cell settingorthorhombic
Space group name H-MI222

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA mismatch repair protein mutL


Mass: 37215.348 Da / Num. of mol.: 1 / Fragment: N-terminal 40KD ATPase fragment (LN40)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: mutL / Plasmid: pET15b pTX418 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 (DE3) / References: UniProt: Q8XDN4, UniProt: P23367*PLUS

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Non-polymers , 5 types, 189 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.64 Å3/Da / Density % sol: 53.1 %
Crystal growTemperature: 293 K / Method: evaporation, recrystallization / pH: 8.2
Details: PEG 4000, ammonium sulfate, potassium choloride, megnesium choloride, DTT, EDTA, pH 8.2, EVAPORATION, RECRYSTALLIZATION, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / Details: Ban, C., (1999) Cell(Cambridge,Mass.), 97, 85.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
16 mg/mlprotein1drop
220 mMTris-HCl1drop
31 mMdithiothreitol1drop
41.0 mMEDTA1drop
5150 mM1dropKCl
65 mM1dropMgCl2
7100 mMTris-HCl1reservoirpH8.2
8150 mMammonium sulfate1reservoirLiSO4
950 mMdithiothreitol1reservoirKCl
1024 %(w/v)PEG40001reservoir
115 mM1reservoirMgCl2
121 mMEDTA1reservoir
131 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 10, 2002 / Details: mirrors
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 55055 / Num. obs: 51448 / % possible obs: 93.4 % / Observed criterion σ(I): -3
Reflection shellResolution: 2→2.03 Å / % possible all: 92
Reflection
*PLUS
Highest resolution: 2 Å / % possible obs: 95.6 % / Rmerge(I) obs: 0.043
Reflection shell
*PLUS
% possible obs: 92 % / Rmerge(I) obs: 0.139

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B63

1b63


Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 2496 5 %RANDOM
Rwork0.208 ---
obs0.2081 51448 93.4 %-
all-55055 --
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2618 0 41 184 2843
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0055
X-RAY DIFFRACTIONc_angle_d1.1306
X-RAY DIFFRACTIONc_angle_deg1.1306
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it1.3521.5
X-RAY DIFFRACTIONc_mcangle_it2.0882
X-RAY DIFFRACTIONc_scbond_it2.2032
X-RAY DIFFRACTIONc_scangle_it3.3312.5
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.117

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