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- PDB-4oc8: DNA modification-dependent restriction endonuclease AspBHI -

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Basic information

Entry
Database: PDB / ID: 4oc8
TitleDNA modification-dependent restriction endonuclease AspBHI
Componentsrestriction endonuclease AspBHI
KeywordsHYDROLASE / DNA Cleavage / DNA Restriction Enzymes / DNA-Binding Proteins / Tetramerization / Models / Molecular / Azoarcus / Protein Multimerization / Protein Structure / Tertiary
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 / Trna Endonuclease; Chain: A, domain 1 - #10 / Trna Endonuclease; Chain: A, domain 1 / tRNA endonuclease-like domain superfamily / Roll ...PUA domain-like - #20 / Restriction endonuclease AspBHI, N-terminal / Restriction endonuclease AspBHI N-terminal / Restriction endonuclease type IV, Mrr / Restriction endonuclease / PUA domain-like / Trna Endonuclease; Chain: A, domain 1 - #10 / Trna Endonuclease; Chain: A, domain 1 / tRNA endonuclease-like domain superfamily / Roll / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Restriction endonuclease
Similarity search - Component
Biological speciesAzoarcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.884 Å
AuthorsHorton, J.R.
CitationJournal: Sci Rep / Year: 2014
Title: Structure and mutagenesis of the DNA modification-dependent restriction endonuclease AspBHI.
Authors: Horton, J.R. / Nugent, R.L. / Li, A. / Mabuchi, M.Y. / Fomenkov, A. / Cohen-Karni, D. / Griggs, R.M. / Zhang, X. / Wilson, G.G. / Zheng, Y. / Xu, S.Y. / Cheng, X.
History
DepositionJan 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 AspBHI
B: restriction endonuclease AspBHI
C: restriction endonuclease AspBHI
D: restriction endonuclease AspBHI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,02212
Polymers171,2624
Non-polymers7608
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12090 Å2
ΔGint-85 kcal/mol
Surface area49550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.092, 195.092, 81.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein
restriction endonuclease AspBHI


Mass: 42815.582 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azoarcus sp. (bacteria) / Strain: BH72 / Gene: azo0355 / Production host: Escherichia coli (E. coli) / References: UniProt: A1K2B7
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 12% polyethylene glycol 3350, 0.5 M K2HPO4/Na2HPO4, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1.06296 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 19, 2010
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06296 Å / Relative weight: 1
ReflectionResolution: 2.89→30.74 Å / Num. all: 40080 / Num. obs: 40065 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 10.9 % / Biso Wilson estimate: 64.14 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 19.7
Reflection shellResolution: 2.89→2.99 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIX(phenix.refine: 1.8_1069)model building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8_1069phasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.884→30.739 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 26.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2352 2011 5.03 %
Rwork0.1971 --
obs0.199 39996 99.79 %
all-39996 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.02 Å2
Refinement stepCycle: LAST / Resolution: 2.884→30.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9402 0 40 53 9495
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049694
X-RAY DIFFRACTIONf_angle_d0.86913228
X-RAY DIFFRACTIONf_dihedral_angle_d12.7133506
X-RAY DIFFRACTIONf_chiral_restr0.061465
X-RAY DIFFRACTIONf_plane_restr0.0031726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8839-2.9560.36811030.27242707X-RAY DIFFRACTION99
2.956-3.03580.34482060.2572619X-RAY DIFFRACTION100
3.0358-3.12510.27921010.24482753X-RAY DIFFRACTION100
3.1251-3.22580.28762040.23612633X-RAY DIFFRACTION100
3.2258-3.3410.27541020.22482743X-RAY DIFFRACTION100
3.341-3.47460.27921000.20872745X-RAY DIFFRACTION100
3.4746-3.63250.26312020.19852649X-RAY DIFFRACTION100
3.6325-3.82370.24881010.19742736X-RAY DIFFRACTION100
3.8237-4.06280.23141960.18332683X-RAY DIFFRACTION100
4.0628-4.37560.1603970.16512731X-RAY DIFFRACTION100
4.3756-4.81450.21871620.15822709X-RAY DIFFRACTION100
4.8145-5.50770.20861460.16762725X-RAY DIFFRACTION100
5.5077-6.9260.2441020.19762788X-RAY DIFFRACTION100
6.926-30.74030.19721890.2132764X-RAY DIFFRACTION100

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