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- PDB-4rzl: DNA recognition domain of the cytosine modification-dependent res... -

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Basic information

Entry
Database: PDB / ID: 4rzl
TitleDNA recognition domain of the cytosine modification-dependent restriction endonuclease LpnPI
ComponentsRestriction endonuclease LpnPI
KeywordsDNA BINDING PROTEIN / cytosine modification / SRA domain / LpnPI / restriction endonuclease / DNA binding
Function / homology
Function and homology information


DNA restriction-modification system / endonuclease activity / DNA binding
Similarity search - Function
PUA domain-like - #20 / Restriction endonuclease AspBHI, N-terminal / Restriction endonuclease AspBHI N-terminal / Restriction endonuclease type IV, Mrr / Restriction endonuclease / PUA domain-like / Roll / Mainly Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSasnauskas, G. / Tamulaitiene, G. / Siksnys, V.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Structure-guided sequence specificity engineering of the modification-dependent restriction endonuclease LpnPI.
Authors: Sasnauskas, G. / Zagorskaite, E. / Kauneckaite, K. / Tamulaitiene, G. / Siksnys, V.
History
DepositionDec 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Sep 20, 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 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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: Restriction endonuclease LpnPI
B: Restriction endonuclease LpnPI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8543
Polymers51,6162
Non-polymers2381
Water7,602422
1
A: Restriction endonuclease LpnPI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0462
Polymers25,8081
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Restriction endonuclease LpnPI


Theoretical massNumber of molelcules
Total (without water)25,8081
Polymers25,8081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.037, 82.037, 152.829
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: -2 - 224 / Label seq-ID: 6 - 232

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein Restriction endonuclease LpnPI


Mass: 25808.082 Da / Num. of mol.: 2 / Fragment: N-terminal domain (UNP residues 2-224)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Strain: Philadelphia 1 / Gene: AAU27318, lpg1234 / Plasmid: pLATE11 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q5ZW53
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 422 / 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: 2.88 Å3/Da / Density % sol: 57.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.16 M (NH4)2SO4, 0.08 M Na-HEPES, 20% w/v PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.0012 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 12, 2014 / Details: mirrors
RadiationMonochromator: Si (111) double crystal monochromator, first crystal indirectly water-cooled
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0012 Å / Relative weight: 1
ReflectionResolution: 2.1→41.4 Å / Num. all: 33984 / Num. obs: 33984 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.9 % / Biso Wilson estimate: 22.34 Å2 / Rsym value: 0.101 / Net I/σ(I): 21.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.2112.80.5241.46364649590.524100
2.21-2.3512.80.3662.16016546840.366100
2.35-2.5112.90.2712.95650043890.271100
2.51-2.7112.90.2063.85314741120.206100
2.71-2.9712.90.1345.84861437550.134100
2.97-3.32130.08494437034240.084100
3.32-3.83130.05712.93899030020.057100
3.83-4.7130.04117.43321125610.041100
4.7-6.6412.90.03917.92568219850.039100
6.64-41.412.50.03217.21386111130.03299.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.547
Highest resolutionLowest resolution
Rotation19.81 Å4 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
MOLREP11.2.05phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
MxCuBEdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4OC8, chain A, residues 6-22, 31-85, 97-208

4oc8


Resolution: 2.1→41.019 Å / SU ML: 0.2 / Isotropic thermal model: Isotropic / σ(F): 1.24 / Phase error: 19.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1986 6585 9.81 %RANDOM
Rwork0.1658 ---
obs0.1691 33923 99.99 %-
all-33984 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.09 Å2 / Biso mean: 26.6084 Å2 / Biso min: 8.59 Å2
Refinement stepCycle: LAST / Resolution: 2.1→41.019 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3490 0 16 422 3928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013600
X-RAY DIFFRACTIONf_angle_d1.0924891
X-RAY DIFFRACTIONf_chiral_restr0.061523
X-RAY DIFFRACTIONf_plane_restr0.006640
X-RAY DIFFRACTIONf_dihedral_angle_d12.3771282
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1994X-RAY DIFFRACTION4.108TORSIONAL
12B1994X-RAY DIFFRACTION4.108TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1-2.12390.25992360.224320282264
2.1239-2.14890.27342050.22220692274
2.1489-2.17510.25822040.202719882192
2.1751-2.20260.30432320.20320022234
2.2026-2.23160.27822080.205320312239
2.2316-2.26220.2362240.203820362260
2.2622-2.29450.2521820.202420322214
2.2945-2.32870.22362400.182620402280
2.3287-2.36510.21372200.170219702190
2.3651-2.40390.21142210.182620362257
2.4039-2.44530.24492360.171920132249
2.4453-2.48980.24182200.186820152235
2.4898-2.53770.2021950.178920042199
2.5377-2.58950.21262160.178120652281
2.5895-2.64580.21362080.171320492257
2.6458-2.70730.21562430.181819892232
2.7073-2.7750.26232000.188219822182
2.775-2.850.23772160.181920532269
2.85-2.93380.20632240.173920292253
2.9338-3.02850.21132310.182820062237
3.0285-3.13670.2262290.174619802209
3.1367-3.26230.20492460.165820242270
3.2623-3.41070.22431790.165320702249
3.4107-3.59040.17892330.151319752208
3.5904-3.81520.15162360.143619842220
3.8152-4.10950.16192130.136220452258
4.1095-4.52260.14352120.119420322244
4.5226-5.17590.13522240.122920122236
5.1759-6.51690.17332250.160419972222
6.5169-41.02630.16232270.164920102237

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