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- PDB-4par: The 5-Hydroxymethylcytosine-Specific Restriction Enzyme AbaSI in ... -

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Basic information

Entry
Database: PDB / ID: 4par
TitleThe 5-Hydroxymethylcytosine-Specific Restriction Enzyme AbaSI in a Complex with Product-like DNA
Components
  • DNA 14-MER
  • DNA 18-MER
  • Uncharacterized protein AbaSI
KeywordsDNA Binding Protein/DNA / Hydroxymethylcytosine-dependent restriction enzyme / hydrolase / VSR endonuclease-like / SRA domain-like / Epigenetic sequencing tool / DNA Binding Protein-DNA complex
Function / homologySET and RING associated domain / : / SET and RING associated domain / Restriction endonuclease PvuRts1 I-like, N-terminal / DNA / DNA (> 10) / Uncharacterized protein
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
T4likevirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsHorton, J.R. / Cheng, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-20 United States
Citation
Journal: Nucleic Acids Res. / Year: 2014
Title: Structure of 5-hydroxymethylcytosine-specific restriction enzyme, AbaSI, in complex with DNA.
Authors: Horton, J.R. / Borgaro, J.G. / Griggs, R.M. / Quimby, A. / Guan, S. / Zhang, X. / Wilson, G.G. / Zheng, Y. / Zhu, Z. / Cheng, X.
#1: Journal: Cell Rep / Year: 2013
Title: High-resolution enzymatic mapping of genomic 5-hydroxymethylcytosine in mouse embryonic stem cells.
Authors: Sun, Z. / Terragni, J. / Jolyon, T. / Borgaro, J.G. / Liu, Y. / Yu, L. / Guan, S. / Wang, H. / Sun, D. / Cheng, X. / Zhu, Z. / Pradhan, S. / Zheng, Y.
#2: Journal: Nucleic Acids Res. / Year: 2013
Title: Characterization of the 5-hydroxymethylcytosine-specific DNA restriction endonucleases.
Authors: Borgaro, J.G. / Zhu, Z.
#3: Journal: Nucleic Acids Res. / Year: 2011
Title: Comparative characterization of the PvuRts1I family of restriction enzymes and their application in mapping genomic 5-hydroxymethylcytosine.
Authors: Wang, H. / Guan, S. / Quimby, A. / Cohen-Karni, D. / Pradhan, S. / Wilson, G. / Roberts, R.J. / Zhu, Z. / Zheng, Y.
History
DepositionApr 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Mar 27, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: DNA 18-MER
G: DNA 14-MER
F: DNA 18-MER
H: DNA 14-MER
B: Uncharacterized protein AbaSI
A: Uncharacterized protein AbaSI
C: Uncharacterized protein AbaSI
D: Uncharacterized protein AbaSI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,4089
Polymers170,3468
Non-polymers621
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12930 Å2
ΔGint-52 kcal/mol
Surface area67900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.826, 144.704, 105.033
Angle α, β, γ (deg.)90.00, 94.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain DNA 18-MER


Mass: 5530.606 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) T4likevirus
#2: DNA chain DNA 14-MER


Mass: 4294.814 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) T4likevirus
#3: Protein
Uncharacterized protein AbaSI


Mass: 37673.785 Da / Num. of mol.: 4 / Mutation: C2S, C309S, C321S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: SDF / Gene: ABSDF3356 / Production host: Escherichia coli (E. coli) / Variant (production host): BL21(DE3) / References: UniProt: B0VN39
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: PEG 3350, ammonium tartrate, HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.89→34.9 Å / Num. obs: 35953 / % possible obs: 98.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 74.5 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 13.4
Reflection shellResolution: 2.89→2.99 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.789 / Mean I/σ(I) obs: 1.4 / % possible all: 89.3

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1593) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: model from 2 SAD expts

Resolution: 2.89→34.9 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2489 1786 4.98 %
Rwork0.1898 --
obs0.1927 35850 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.89→34.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10386 1304 4 0 11694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512065
X-RAY DIFFRACTIONf_angle_d0.89416555
X-RAY DIFFRACTIONf_dihedral_angle_d17.5434654
X-RAY DIFFRACTIONf_chiral_restr0.0361812
X-RAY DIFFRACTIONf_plane_restr0.0041887
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.889-2.9670.36911190.30562204X-RAY DIFFRACTION84
2.967-3.05430.36291290.30922548X-RAY DIFFRACTION95
3.0543-3.15280.36061340.28942605X-RAY DIFFRACTION98
3.1528-3.26540.32751470.24392647X-RAY DIFFRACTION99
3.2654-3.39610.26191410.22552637X-RAY DIFFRACTION99
3.3961-3.55050.29891360.22332656X-RAY DIFFRACTION100
3.5505-3.73750.33211290.21772677X-RAY DIFFRACTION100
3.7375-3.97130.28491470.19482664X-RAY DIFFRACTION100
3.9713-4.27740.2591420.17782684X-RAY DIFFRACTION100
4.2774-4.7070.17881390.15932666X-RAY DIFFRACTION100
4.707-5.38590.23461420.16142672X-RAY DIFFRACTION100
5.3859-6.77760.24991420.18532706X-RAY DIFFRACTION100
6.7776-34.90210.17421390.15062698X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.1031-0.49781.21333.48111.581610.93350.18950.7408-0.1740.01680.5228-0.756-0.19881.0304-0.67240.33130.0297-0.07650.4787-0.14840.66740.959911.4715-32.8951
24.0274-0.02321.21474.9234-1.41556.89740.3685-1.22580.01911.405-0.0523-0.5212-0.3984-0.0506-0.34390.89430.0057-0.16651.0222-0.05390.63762.275316.7414-6.1673
37.0025-0.11182.20332.87850.03939.90730.0222-0.4592-0.15610.03840.27550.20880.0306-0.9373-0.27850.3283-0.0731-0.03580.35930.05660.5574-23.03059.0888-45.7059
46.8317-0.57520.68695.53561.34117.94010.21041.0802-0.1199-1.10310.16860.1081-0.4730.0121-0.37830.5897-0.04480.00360.56080.0020.3633-27.111816.3425-72.4956
54.31040.3283-3.45993.77971.90335.6220.1671-0.45340.8356-0.25120.33240.0725-0.39180.9196-0.51190.4395-0.09560.04570.4747-0.01490.6901-5.076857.4082-24.4687
63.00210.0247-0.47972.09243.11417.66940.2129-0.74360.67840.37380.3223-0.46870.09811.745-0.55180.6071-0.1056-0.01241.1278-0.15130.89123.71556.549-19.1069
74.17730.7127-0.55364.66150.07889.11940.09770.36120.2002-1.0294-0.1448-0.52320.27061.27060.01830.68390.08380.13980.66350.19770.59221.590850.4169-48.0379
87.764-0.2598-2.44545.74310.08239.8223-0.04320.62020.0455-0.01360.47750.48980.34-0.8112-0.43480.3801-0.06-0.01580.45070.01190.5387-25.749458.2206-10.5853
94.4222-0.0487-1.31222.3672-0.55617.1899-0.0249-1.30650.38811.2790.2629-0.11880.01870.511-0.2491.07050.138-0.02990.845-0.22070.646-26.393356.452816.1491
102.8281-1.25442.03344.01782.10315.79510.491.08350.3357-0.39130.2367-0.16450.6247-0.4606-0.73590.81410.03930.10260.88630.15590.573-9.839834.2737-62.1746
113.3065-1.0106-1.6891.3004-0.21234.29030.41661.4768-0.132-0.9599-0.32560.0649-0.1466-1.1282-0.26381.21270.05560.18011.36410.01850.6197-7.609534.324-73.2557
121.45220.183-0.67730.8211-0.52681.50870.6026-1.601-0.3007-0.00780.43950.2419-2.7737-1.0021-1.07041.93070.20410.1421.71940.05140.7235-12.944235.455-9.019
131.5503-1.88370.70781.3385-0.4954.5331-0.1158-0.79540.03850.36830.7215-0.023-0.44860.0634-0.59841.71250.07910.05750.9903-0.06540.6125-12.700632.4449-17.9019
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 5:151)
2X-RAY DIFFRACTION2(chain A and resid 152:318)
3X-RAY DIFFRACTION3(chain B and resid 5:173)
4X-RAY DIFFRACTION4(chain B and resid 174:317)
5X-RAY DIFFRACTION5(chain C and resid 4:78)
6X-RAY DIFFRACTION6(chain C and resid 79:151)
7X-RAY DIFFRACTION7(chain C and resid 152:317)
8X-RAY DIFFRACTION8(chain D and resid 5:150)
9X-RAY DIFFRACTION9(chain D and resid 151:317)
10X-RAY DIFFRACTION10(chain E and resid 1:30)
11X-RAY DIFFRACTION11(chain E and resid 31:42)
12X-RAY DIFFRACTION12(chain F and resid 1:13)
13X-RAY DIFFRACTION13(chain F and resid 14:42)

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