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- PDB-4xqk: ATP-dependent Type ISP restriction-modification enzyme LlaBIII bo... -

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Basic information

Entry
Database: PDB / ID: 4xqk
TitleATP-dependent Type ISP restriction-modification enzyme LlaBIII bound to DNA
Components
  • (DNA (28-MER)) x 2
  • LlaBIII
KeywordsHYDROLASE/DNA / ATP-dependent restriction-modification enzyme / Type ISP restriction-modification enzyme / ATPase / HYDROLASE-DNA complex
Function / homology
Function and homology information


N-methyltransferase activity / : / hydrolase activity / DNA binding / ATP binding
Similarity search - Function
Mrr-like domain / Restriction endonuclease / Type ISP restriction-modification enzyme LLaBIII, C-terminal specificity domain / Type ISP C-terminal specificity domain / N-6 DNA Methylase / DNA methylase, adenine-specific / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / Restriction endonuclease type II-like / Helicase conserved C-terminal domain ...Mrr-like domain / Restriction endonuclease / Type ISP restriction-modification enzyme LLaBIII, C-terminal specificity domain / Type ISP C-terminal specificity domain / N-6 DNA Methylase / DNA methylase, adenine-specific / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / Restriction endonuclease type II-like / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / DNA / DNA (> 10) / LlaBIII
Similarity search - Component
Biological speciesLactococcus lactis subsp. cremoris (lactic acid bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsChand, M.K. / Saikrishnan, K.
Funding support India, 1items
OrganizationGrant numberCountry
Wellcome Trust-DBT India Alliance500048-Z-09-Z India
CitationJournal: Nat.Chem.Biol. / Year: 2015
Title: Translocation-coupled DNA cleavage by the Type ISP restriction-modification enzymes
Authors: Chand, M.K. / Nirwan, N. / Diffin, F.M. / Aelst, K.V. / Kulkarni, M. / Pernstich, C. / Szczelkun, M.D. / Saikrishnan, K.
History
DepositionJan 19, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Data collection
Revision 1.2Nov 4, 2015Group: Database references
Revision 1.3Feb 5, 2020Group: Data collection / Derived calculations / Source and taxonomy
Category: diffrn_source / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_entity_src_syn.ncbi_taxonomy_id ..._diffrn_source.pdbx_synchrotron_site / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LlaBIII
B: LlaBIII
C: DNA (28-MER)
D: DNA (28-MER)
E: DNA (28-MER)
F: DNA (28-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)394,9059
Polymers394,7876
Non-polymers1173
Water2,666148
1
A: LlaBIII
C: DNA (28-MER)
D: DNA (28-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,4725
Polymers197,3943
Non-polymers782
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8490 Å2
ΔGint-37 kcal/mol
Surface area69160 Å2
MethodPISA
2
B: LlaBIII
E: DNA (28-MER)
F: DNA (28-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,4334
Polymers197,3943
Non-polymers391
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8250 Å2
ΔGint-45 kcal/mol
Surface area67960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.880, 112.660, 146.210
Angle α, β, γ (deg.)103.30, 90.88, 105.79
Int Tables number1
Space group name H-MP1

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Components

#1: Protein LlaBIII


Mass: 180181.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. cremoris (lactic acid bacteria)
Strain: W10 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M3KL05*PLUS
#2: DNA chain DNA (28-MER)


Mass: 8541.505 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (28-MER)


Mass: 8670.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: potassium chloride, PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9793 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 102869 / % possible obs: 96.4 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 11.2
Reflection shellResolution: 2.7→2.77 Å / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.2 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→48.216 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 31.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2597 4969 5.01 %
Rwork0.2185 94912 -
obs0.2206 99188 96.47 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→48.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23312 2283 3 148 25746
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00326316
X-RAY DIFFRACTIONf_angle_d0.68236161
X-RAY DIFFRACTIONf_dihedral_angle_d17.4779701
X-RAY DIFFRACTIONf_chiral_restr0.034099
X-RAY DIFFRACTIONf_plane_restr0.0034265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.73070.33161590.31193165X-RAY DIFFRACTION97
2.7307-2.76280.37831460.32783122X-RAY DIFFRACTION96
2.7628-2.79650.38451500.32233115X-RAY DIFFRACTION97
2.7965-2.83190.37391700.3233170X-RAY DIFFRACTION97
2.8319-2.86910.39361840.30773134X-RAY DIFFRACTION96
2.8691-2.90840.34871720.30243130X-RAY DIFFRACTION97
2.9084-2.950.35611490.30023188X-RAY DIFFRACTION97
2.95-2.9940.30861620.28543217X-RAY DIFFRACTION97
2.994-3.04080.3491440.28733116X-RAY DIFFRACTION97
3.0408-3.09060.36131760.27663117X-RAY DIFFRACTION97
3.0906-3.14390.32611880.27063202X-RAY DIFFRACTION96
3.1439-3.20110.30161630.25553081X-RAY DIFFRACTION96
3.2011-3.26260.31681440.25963192X-RAY DIFFRACTION98
3.2626-3.32920.32071690.25723202X-RAY DIFFRACTION97
3.3292-3.40160.29911680.25563121X-RAY DIFFRACTION97
3.4016-3.48070.28541890.24173134X-RAY DIFFRACTION97
3.4807-3.56770.29671620.23033092X-RAY DIFFRACTION97
3.5677-3.66410.30591780.23973190X-RAY DIFFRACTION97
3.6641-3.77190.27311560.21823138X-RAY DIFFRACTION97
3.7719-3.89360.23561690.20993139X-RAY DIFFRACTION96
3.8936-4.03270.22341540.20083135X-RAY DIFFRACTION96
4.0327-4.19410.21211790.19173187X-RAY DIFFRACTION97
4.1941-4.38480.22721740.18443089X-RAY DIFFRACTION96
4.3848-4.61590.20241800.17353098X-RAY DIFFRACTION96
4.6159-4.90480.21751740.17893179X-RAY DIFFRACTION97
4.9048-5.28310.23141460.19543153X-RAY DIFFRACTION97
5.2831-5.81390.23051640.20673151X-RAY DIFFRACTION97
5.8139-6.65330.26891810.21383086X-RAY DIFFRACTION95
6.6533-8.37530.23291650.19533086X-RAY DIFFRACTION95
8.3753-48.22340.19581540.16953090X-RAY DIFFRACTION94

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