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- PDB-3zi5: Crystal STRUCTURE OF RESTRICTION ENDONUCLEASE BFII C-TERMINAL REC... -

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Basic information

Entry
Database: PDB / ID: 3zi5
TitleCrystal STRUCTURE OF RESTRICTION ENDONUCLEASE BFII C-TERMINAL RECOGNITION DOMAIN IN COMPLEX WITH COGNATE DNA
Components
  • 5'-D(*AP*GP*CP*AP*CP*TP*GP*GP*GP*TP*CP*GP)-3'
  • 5'-D(*CP*GP*AP*CP*CP*CP*AP*GP*TP*GP*CP*TP)-3'
  • RESTRICTION ENDONUCLEASE
KeywordsHYDROLASE/DNA / HYDROLASE-DNA COMPLEX / DNA-BINDING PSEUDOBARREL FOLD / DNA RECOGNITION
Function / homology
Function and homology information


endonuclease activity
Similarity search - Function
At1g16640 B3 domain - #30 / Restriction endonuclease BfiI C-terminal domain / Metal-independent restriction enzyme BfiI, DNA binding domain / Metal-independent restriction enzyme BfiI DNA binding domain / At1g16640 B3 domain / Phospholipase D-like domain / PLD-like domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Restriction endonuclease
Similarity search - Component
Biological speciesBACILLUS FIRMUS (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsGolovenko, D. / Manakova, E. / Zakrys, L. / Zaremba, M. / Sasnauskas, G. / Grazulis, S. / Siksnys, V.
Citation
Journal: Nucleic Acids Res. / Year: 2014
Title: Structural Insight Into the Specificity of the B3 DNA-Binding Domains Provided by the Co-Crystal Structure of the C-Terminal Fragment of Bfii Restriction Enzyme
Authors: Golovenko, D. / Grazulis, S. / Manakova, E. / Sasnauskas, G. / Siksnys, V. / Zakrys, L. / Zaremba, M.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Structure of the Metal-Independent Restriction Enzyme Bfii Reveals Fusion of a Specific DNA-Binding Domain with a Nonspecific Nuclease.
Authors: Grazulis, S. / Manakova, E. / Roessle, M. / Bochtler, M. / Tamulaitiene, G. / Huber, R. / Siksnys, V.
History
DepositionJan 3, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Apr 16, 2014Group: Database references
Revision 1.3May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / pdbx_unobs_or_zero_occ_atoms / struct_biol
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RESTRICTION ENDONUCLEASE
B: 5'-D(*AP*GP*CP*AP*CP*TP*GP*GP*GP*TP*CP*GP)-3'
C: 5'-D(*CP*GP*AP*CP*CP*CP*AP*GP*TP*GP*CP*TP)-3'
D: RESTRICTION ENDONUCLEASE
E: 5'-D(*AP*GP*CP*AP*CP*TP*GP*GP*GP*TP*CP*GP)-3'
F: 5'-D(*CP*GP*AP*CP*CP*CP*AP*GP*TP*GP*CP*TP)-3'


Theoretical massNumber of molelcules
Total (without water)52,0636
Polymers52,0636
Non-polymers00
Water50428
1
A: RESTRICTION ENDONUCLEASE
B: 5'-D(*AP*GP*CP*AP*CP*TP*GP*GP*GP*TP*CP*GP)-3'
C: 5'-D(*CP*GP*AP*CP*CP*CP*AP*GP*TP*GP*CP*TP)-3'


Theoretical massNumber of molelcules
Total (without water)26,0323
Polymers26,0323
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-21 kcal/mol
Surface area10310 Å2
MethodPISA
2
D: RESTRICTION ENDONUCLEASE
E: 5'-D(*AP*GP*CP*AP*CP*TP*GP*GP*GP*TP*CP*GP)-3'
F: 5'-D(*CP*GP*AP*CP*CP*CP*AP*GP*TP*GP*CP*TP)-3'


Theoretical massNumber of molelcules
Total (without water)26,0323
Polymers26,0323
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-17 kcal/mol
Surface area10300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.180, 175.180, 35.789
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein RESTRICTION ENDONUCLEASE / R.BFII


Mass: 18704.820 Da / Num. of mol.: 2 / Fragment: DNA BINDING DOMAIN BFII-C, RESIDUES 193-358
Source method: isolated from a genetically manipulated source
Details: PROTEOLYTIC FRAGMENT OF R.BFIIK107A SPANNING RESIDUES 193-358
Source: (gene. exp.) BACILLUS FIRMUS (bacteria) / Strain: S8120 / Plasmid: PET21B-BFIIK107A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ER2566
References: UniProt: Q9F4C9, type II site-specific deoxyribonuclease
#2: DNA chain 5'-D(*AP*GP*CP*AP*CP*TP*GP*GP*GP*TP*CP*GP)-3' / UPPER DNA STRAND


Mass: 3703.416 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*CP*GP*AP*CP*CP*CP*AP*GP*TP*GP*CP*TP)-3' / BOTTOM DNA STRAND


Mass: 3623.368 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IS DESCRIBED IN SAPRANAUSKAS ET AL. (2000) J. BIOL.CHEM., 275, P.30878

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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: 2.41 Å3/Da / Density % sol: 58.6 % / Description: NONE
Crystal growTemperature: 292 K
Details: CRYSTALS WERE GROWN AT 19C BY MIXING COMPLEX SOLUTION WITH THE CRYSTALLIZATION BUFFER 0.49 M NAH2PO4, 0.91 M K2HPO4 (PH6.9 AT 25C).

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Sep 22, 2009 / Details: OSMIC CONFOCAL MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→50.57 Å / Num. obs: 10809 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 6.97 % / Biso Wilson estimate: 24.38 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 13.31
Reflection shellResolution: 3.2→3.23 Å / Redundancy: 6.49 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5.43 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
TRUNCATEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C1L CHAIN A RESIDUES 200-358

2c1l


Resolution: 3.2→43.795 Å / SU ML: 0.31 / σ(F): 1.35 / Phase error: 20.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2259 1040 9.6 %
Rwork0.1757 --
obs0.1805 10790 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→43.795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2642 972 0 28 3642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033784
X-RAY DIFFRACTIONf_angle_d0.7435324
X-RAY DIFFRACTIONf_dihedral_angle_d20.8821446
X-RAY DIFFRACTIONf_chiral_restr0.029588
X-RAY DIFFRACTIONf_plane_restr0.003528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2002-3.36890.26521340.20031369X-RAY DIFFRACTION100
3.3689-3.57990.26571330.18831413X-RAY DIFFRACTION100
3.5799-3.85610.25191670.18111342X-RAY DIFFRACTION100
3.8561-4.24390.21871480.1631370X-RAY DIFFRACTION100
4.2439-4.85730.18671410.13811387X-RAY DIFFRACTION100
4.8573-6.11710.19561510.16541415X-RAY DIFFRACTION100
6.1171-43.79910.22221660.20781454X-RAY DIFFRACTION100
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)
16.0106-0.07783.62481.99661.03254.5037-0.06430.4642-0.0810.034-0.15720.1110.0280.27310.16620.2791-0.0120.03130.30120.0110.2968-77.528711.3842.1979
21.1249-0.7398-0.23923.4809-1.5632.3288-0.1661-0.3167-0.0254-0.43440.0151-0.4428-0.0575-0.13140.22390.3375-0.09370.02460.3514-0.05590.2679-70.1810.778-3.0125
37.7678-2.3434-0.15722.3747-2.11649.7925-0.0790.3936-0.5133-0.18590.1877-1.15480.36161.7262-0.02220.4080.05810.01470.440.10240.6768-54.361712.3899-6.3263
44.9508-2.2491-1.34894.20481.37571.544-0.32370.51310.47021.0281-0.0199-0.44390.7668-0.240.32540.3982-0.0518-0.1470.34920.04810.3534-68.968418.2607-3.2259
58.15040.4642-0.39468.8376-5.364.3662-0.2649-0.60131.41191.35040.837-0.7825-1.0160.1841-0.9670.593-0.00520.07550.2455-0.05950.3697-77.332222.97418.9111
66.6371-4.341-4.05824.01274.72666.14090.1230.2189-0.1025-1.01880.1870.2386-0.71430.0272-0.37950.42540.0407-0.01490.37430.06040.3564-65.622511.0849-4.7373
72.5934-1.01272.08652.19130.63153.11780.0059-0.3360.23220.0007-0.0145-0.14210.0074-0.1984-0.05650.2653-0.0360.04830.2688-0.0280.3299-77.323214.83594.0311
85.2282-1.20843.80082.0007-2.05352.8889-0.48480.52060.0147-0.23660.9570.41270.65860.2237-0.32520.31880.0790.16920.45490.04440.505-90.17449.1339.8653
96.4401-3.7566-2.24168.87941.94693.9365-0.33890.4048-0.9652-0.2380.11131.31320.5492-0.20080.26920.4047-0.1088-0.08160.3382-0.02610.2984-85.39955.0221-2.4237
102.2763-2.0291-0.06735.9775-1.24092.0480.67590.59071.239-1.4762-0.09620.7172-0.6942-0.752-0.19680.60860.0721-0.0150.44650.03820.588-92.60219.8725-0.694
115.63962.9879-0.43746.3879-2.00050.6759-0.1354-0.1761-0.3187-0.7791-0.1008-0.4183-0.0229-0.03560.19990.3270.0533-0.00690.38170.01980.2281-62.00792.5981.8878
126.023-0.07431.36190.3743-1.45155.50840.1265-0.23660.1128-0.3254-0.0414-0.46490.19910.1747-0.20690.43460.07990.02860.2621-0.00660.5228-61.98753.04581.4342
131.4734-1.37-0.38894.80272.76792.9713-0.2546-0.1772-0.30250.1086-0.14060.7783-0.56830.11850.12410.41220.01720.02310.34650.07010.4355-65.167641.4521-15.7528
142.57232.7231-1.67923.0237-1.47171.55620.0986-0.1376-0.0057-0.0963-0.09160.04850.12370.24220.00750.43730.0508-0.06910.32190.00620.3309-58.884336.34-11.9348
154.19954.4096-4.85214.9276-5.43275.98620.2274-0.3797-0.7598-0.7989-0.1017-0.9878-0.1830.5419-0.54450.55090.0287-0.11390.3455-0.0890.4701-51.527422.2771-8.2027
165.3777-1.93022.57943.1037-1.04543.2169-1.0535-0.2186-0.00760.00770.64440.0047-0.26140.00670.02310.4105-0.0971-0.06650.29790.0310.3247-61.313430.1957-10.8582
176.37893.1858-7.45088.4495-6.79482.00110.37070.7912-0.44910.44710.35920.65821.079-1.4027-0.5990.8125-0.2374-0.2570.45490.09070.5181-72.746732.3244-23.1638
189.85954.0761.96344.31024.1184.5704-0.1014-0.32210.0525-0.01770.54550.47420.1782-0.4177-0.2470.4927-0.2125-0.01870.45360.16190.5268-58.760630.4246-10.2723
194.33341.4176-1.50613.55441.01721.7490.18870.21170.3383-0.42320.05720.44930.1535-0.2931-0.27280.34630.0002-0.06810.321400.2665-62.171939.0701-17.5229
202.4189-1.43411.11433.8513-0.72533.44710.20860.48540.13360.1554-0.17731.031-0.5285-0.2083-0.23890.4422-0.0671-0.08470.41580.07910.7018-71.919846.4895-16.8297
214.78822.9797-1.5014.5429-0.82592.1038-0.2462-0.14240.3258-0.87380.1555-0.14250.13690.14030.18440.6599-0.05280.06030.1681-0.06080.4292-58.428852.3128-9.7556
223.89023.13570.66056.5921-0.78453.81920.1088-0.44761.8410.0957-0.11721.89910.3364-0.3610.04370.54720.02690.09830.2902-0.01870.739-73.500347.5954-11.879
233.8917-0.50160.23395.7427-2.71681.27220.47950.0239-0.13020.1165-0.5657-0.86-0.15110.3030.12350.461-0.08860.08990.49640.03520.2475-47.808236.232-16.3238
244.587-2.3448-0.55225.4139-0.07053.99530.0892-0.0139-0.5060.1966-0.189-0.38140.24170.22490.09170.3929-0.0588-0.00230.41980.05940.4156-47.926836.045-15.6797
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 193:219)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 220:243)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 244:250)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 251:261)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 262:267)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 268:283)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 284:317)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 318:323)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 324:347)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 348:358)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 1:12)
12X-RAY DIFFRACTION12(CHAIN C AND RESID 1:12)
13X-RAY DIFFRACTION13(CHAIN D AND RESID 193:218)
14X-RAY DIFFRACTION14(CHAIN D AND RESID 219:243)
15X-RAY DIFFRACTION15(CHAIN D AND RESID 244:247)
16X-RAY DIFFRACTION16(CHAIN D AND RESID 248:262)
17X-RAY DIFFRACTION17(CHAIN D AND RESID 263:267)
18X-RAY DIFFRACTION18(CHAIN D AND RESID 268:278)
19X-RAY DIFFRACTION19(CHAIN D AND RESID 279:308)
20X-RAY DIFFRACTION20(CHAIN D AND RESID 309:330)
21X-RAY DIFFRACTION21(CHAIN D AND RESID 331:337)
22X-RAY DIFFRACTION22(CHAIN D AND RESID 338:358)
23X-RAY DIFFRACTION23(CHAIN E AND RESID 1:12)
24X-RAY DIFFRACTION24(CHAIN F AND RESID 1:12)

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