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- PDB-2ge5: EcoRV Restriction Endonuclease C-terminal deletion mutant/GATATC/Ca2+ -

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Basic information

Entry
Database: PDB / ID: 2ge5
TitleEcoRV Restriction Endonuclease C-terminal deletion mutant/GATATC/Ca2+
Components
  • 5'-D(*AP*AP*AP*GP*AP*TP*AP*TP*CP*TP*T)-3'
  • Type II restriction enzyme EcoRV
KeywordsHYDROLASE/DNA / Protein-DNA complex / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / DNA binding / metal ion binding
Similarity search - Function
Restriction endonuclease, type II, EcoRV / Restriction endonuclease, type II, EcoRV, Proteobacteria / Restriction endonuclease EcoRV / 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) / Type II restriction enzyme EcoRV
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHiller, D.A. / Perona, J.J.
Citation
Journal: Biochemistry / Year: 2006
Title: Positively Charged C-Terminal Subdomains of EcoRV Endonuclease: Contributions to DNA Binding, Bending, and Cleavage.
Authors: Hiller, D.A. / Perona, J.J.
#1: Journal: Embo J. / Year: 1993
Title: The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments
Authors: Winkler, F.K. / Banner, D.W. / Oefner, C. / Tsernoglou, D. / Brown, R.S. / Heathman, S.P. / Bryan, R.K. / Martin, P.D. / Petratos, K. / Wilson, K.S.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Crystallographic snapshots along a protein-induced DNA-bending pathway
Authors: Horton, N.C. / Perona, J.J.
History
DepositionMar 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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
C: 5'-D(*AP*AP*AP*GP*AP*TP*AP*TP*CP*TP*T)-3'
D: 5'-D(*AP*AP*AP*GP*AP*TP*AP*TP*CP*TP*T)-3'
A: Type II restriction enzyme EcoRV
B: Type II restriction enzyme EcoRV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4305
Polymers57,3904
Non-polymers401
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.101, 67.101, 259.892
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: DNA chain 5'-D(*AP*AP*AP*GP*AP*TP*AP*TP*CP*TP*T)-3'


Mass: 3356.235 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein Type II restriction enzyme EcoRV / E.C.3.1.21.4 / Endonuclease EcoRV / R.EcoRV


Mass: 25338.566 Da / Num. of mol.: 2 / Fragment: residues 1-219
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ecoRVR / Plasmid: pBSRV / Production host: Escherichia coli (E. coli) / Strain (production host): mm294
References: UniProt: P04390, type II site-specific deoxyribonuclease
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.53 Å3/Da / Density % sol: 51.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 250 mM NaCl, 8-12% PEG 4k, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1NaClSodium chloride11
2PEG 4k11
3H2O11
4NaClSodium chloride12
5PEG 4k12
6H2O12

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.97976
DetectorDate: Apr 9, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97976 Å / Relative weight: 1
ReflectionResolution: 2.4→46.677 Å / Num. obs: 16007 / % possible obs: 65.9 % / Redundancy: 6 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 8.6
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRsym value% possible all
2.4-2.5320.73.10.4671.621636940.46745.1
2.53-2.6831.54.50.3582.1463610240.358
2.68-2.8745.15.40.2413.1740013670.241
2.87-3.164.55.80.1614.61069418400.161
3.1-3.39956.50.1056.51659325340.105
3.39-3.7999.36.70.0881622824160.08
3.79-4.38996.60.0599.71398921350.059
4.38-5.3797.56.20.04911.71134118200.049
5.37-7.5994.26.50.04912910613990.049
7.59-46.6887.85.80.04214.645507780.042

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Phasing

Phasing MRMethod rotation: fast direct

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
CNSrefinement
PDB_EXTRACT1.701data extraction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1EOP

1eop


Resolution: 2.4→50 Å / FOM work R set: 0.798 / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.284 2692 6.1 %Random
Rwork0.223 ---
obs-15998 64.1 %-
Solvent computationBsol: 38.025 Å2
Displacement parametersBiso mean: 49.368 Å2
Baniso -1Baniso -2Baniso -3
1--9.231 Å20 Å20 Å2
2---9.231 Å20 Å2
3---18.462 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3475 446 1 45 3967
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.23
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.4-2.420.34870.341102109
2.42-2.430.365100.319115125
2.43-2.450.58980.304128136
2.45-2.470.288180.35141159
2.47-2.490.396170.339148165
2.49-2.50.467140.335167181
2.5-2.520.442280.296161189
2.52-2.540.206100.238213223
2.54-2.560.471240.275207231
2.56-2.590.402230.306200223
2.59-2.610.356280.288229257
2.61-2.630.272300.208242272
2.63-2.650.307310.252257288
2.65-2.680.366250.287273298
2.68-2.70.382440.291270314
2.7-2.730.298230.237322345
2.73-2.760.186150.245334349
2.76-2.780.444340.258325359
2.78-2.810.307380.278372410
2.81-2.850.344470.266367414
2.85-2.880.311450.238371416
2.88-2.910.245390.261427466
2.91-2.950.325590.232429488
2.95-2.980.3720.233481553
2.98-3.020.354480.239515563
3.02-3.070.3500.238584634
3.07-3.110.324510.264648699
3.11-3.160.298730.222667740
3.16-3.20.27730.251725798
3.2-3.260.351950.217807902
3.26-3.310.27820.221760842
3.31-3.370.31900.235819909
3.37-3.440.296860.225770856
3.44-3.510.284910.216798889
3.51-3.580.329740.209786860
3.58-3.670.269830.24800883
3.67-3.760.313820.237798880
3.76-3.860.29650.214808873
3.86-3.980.235790.196823902
3.98-4.10.209830.161750833
4.1-4.250.252900.215801891
4.25-4.420.248950.183781876
4.42-4.620.197780.181783861
4.62-4.860.257890.212783872
4.86-5.170.271810.226781862
5.17-5.570.208580.211697755
5.57-6.130.395820.24769851
6.13-7.010.38840.259773857
7.01-8.830.334680.242792860
8.83-500.254730.239652725
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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