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- PDB-5o63: Crystal structure of UbaLAI restriction endonuclease B3 domain do... -

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Basic information

Entry
Database: PDB / ID: 5o63
TitleCrystal structure of UbaLAI restriction endonuclease B3 domain domain (mutant L24M L53M L95M) with cognate DNA
Components
  • DNA (5'-D(*C*G*C*C*A*G*G*G*C*)-3')
  • DNA (5'-D(*G*C*C*C*T*G*G*C*G*)-3')
  • Restriction endonuclease UbaLAI
KeywordsHYDROLASE / restriction endonuclease / B3 domain / protein-DNA complex
Function / homologyDNA
Function and homology information
Biological speciesunidentified (others)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.6 Å
AuthorsTamulaitiene, G. / Sasnauskas, G. / Siksnys, V.
Funding supportLithuania, 1items
OrganizationGrant numberCountry
Research Council of LithuaniaMIP-81/2010Lithuania
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: UbaLAI is a monomeric Type IIE restriction enzyme.
Authors: Sasnauskas, G. / Tamulaitiene, G. / Tamulaitis, G. / Calyseva, J. / Laime, M. / Rimseliene, R. / Lubys, A. / Siksnys, V.
History
DepositionJun 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Restriction endonuclease UbaLAI
B: Restriction endonuclease UbaLAI
C: DNA (5'-D(*C*G*C*C*A*G*G*G*C*)-3')
D: DNA (5'-D(*G*C*C*C*T*G*G*C*G*)-3')
E: DNA (5'-D(*C*G*C*C*A*G*G*G*C*)-3')
F: DNA (5'-D(*G*C*C*C*T*G*G*C*G*)-3')


Theoretical massNumber of molelcules
Total (without water)52,9206
Polymers52,9206
Non-polymers00
Water7,548419
1
A: Restriction endonuclease UbaLAI
C: DNA (5'-D(*C*G*C*C*A*G*G*G*C*)-3')
D: DNA (5'-D(*G*C*C*C*T*G*G*C*G*)-3')


Theoretical massNumber of molelcules
Total (without water)26,4603
Polymers26,4603
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-16 kcal/mol
Surface area9770 Å2
MethodPISA
2
B: Restriction endonuclease UbaLAI
E: DNA (5'-D(*C*G*C*C*A*G*G*G*C*)-3')
F: DNA (5'-D(*G*C*C*C*T*G*G*C*G*)-3')


Theoretical massNumber of molelcules
Total (without water)26,4603
Polymers26,4603
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-15 kcal/mol
Surface area10110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.775, 94.583, 123.403
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Restriction endonuclease UbaLAI


Mass: 20985.578 Da / Num. of mol.: 2 / Fragment: N-terminal B3 DNA binding domain
Source method: isolated from a genetically manipulated source
Details: Environmental DNA sample / Source: (gene. exp.) unidentified (others) / Plasmid: pBAD24
Details (production host): UbaLAI N-terminal domain (residues 1-164), C-terminal His-tag
Production host: Escherichia coli (E. coli) / Variant (production host): DH10B / References: type II site-specific deoxyribonuclease
#2: DNA chain DNA (5'-D(*C*G*C*C*A*G*G*G*C*)-3')


Mass: 2732.786 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*G*C*C*C*T*G*G*C*G*)-3')


Mass: 2741.800 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.: 419 / 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: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: Crystallization buffer was 0.15 M Na-Citrate (pH 5.6), 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.82661 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82661 Å / Relative weight: 1
ReflectionResolution: 1.346→94.583 Å / Num. obs: 63722 / % possible obs: 99.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 21.07 Å2 / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.016 / Rrim(I) all: 0.04 / Rsym value: 0.035 / Net I/av σ(I): 11.1 / Net I/σ(I): 25.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
1.6-1.696.70.4431.80.1960.5150.44399.7
1.69-1.796.80.26230.1160.3050.26299.6
1.79-1.916.40.164.90.0730.1880.1699.7
1.91-2.076.70.0938.20.0420.1090.09399.3
2.07-2.266.80.061120.0270.0710.06199.7
2.26-2.536.30.04316.50.020.0510.04399.7
2.53-2.926.90.03121.50.0140.0360.03199.9
2.92-3.586.50.024200.0110.0280.02499.4
3.58-5.066.60.0225.80.0090.0240.0299.2
5.06-94.58360.02117.40.010.0240.02199.5

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Phasing

PhasingMethod: SIRAS

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Processing

Software
NameVersionClassification
SCALA3.2.19data scaling
SHELXphasing
Cootmodel building
PHENIX1.8.3refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: SIRAS / Resolution: 1.6→51.678 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.31 / Phase error: 19.03
RfactorNum. reflection% reflection
Rfree0.1906 12080 10.01 %
Rwork0.1593 --
obs0.1624 63634 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 78.61 Å2 / Biso mean: 29.4586 Å2 / Biso min: 12.52 Å2
Refinement stepCycle: final / Resolution: 1.6→51.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2516 726 0 419 3661
Biso mean---36.82 -
Num. residues----356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0193689
X-RAY DIFFRACTIONf_angle_d1.7715189
X-RAY DIFFRACTIONf_chiral_restr0.099558
X-RAY DIFFRACTIONf_plane_restr0.011546
X-RAY DIFFRACTIONf_dihedral_angle_d19.5951423
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.61820.28283960.23183590398699
1.6182-1.63720.27793960.21933705410199
1.6372-1.65720.24324130.208336034016100
1.6572-1.67820.24413830.20063645402899
1.6782-1.70030.22993880.19336864074100
1.7003-1.72350.20833870.18123609399699
1.7235-1.74820.22793980.17453637403599
1.7482-1.77430.21974590.18093616407599
1.7743-1.8020.23064000.183935713971100
1.802-1.83150.19533970.171736834080100
1.8315-1.86310.21953910.167636394030100
1.8631-1.8970.20584070.16183595400299
1.897-1.93350.20764020.16043536393897
1.9335-1.9730.21863510.15863648399999
1.973-2.01590.17513880.153536604048100
2.0159-2.06270.22293990.162936264025100
2.0627-2.11430.19174350.16233580401599
2.1143-2.17150.20684640.162935864050100
2.1715-2.23540.18694110.162436194030100
2.2354-2.30760.19773800.159836384018100
2.3076-2.390.20554480.16513620406899
2.39-2.48570.21443710.16433587395898
2.4857-2.59880.20974260.16423622404899
2.5988-2.73590.19114300.166336274057100
2.7359-2.90730.19363720.169837024074100
2.9073-3.13170.21183870.168336444031100
3.1317-3.44680.18894060.15953572397899
3.4468-3.94540.16924080.14553525393397
3.9454-4.97020.14763660.127436884054100
4.9702-51.70450.15324210.14883592401399
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)
11.03860.85970.09241.797-0.59582.5115-0.0380.0427-0.1291-0.03140.0033-0.0880.36030.0612-0.00770.17090.00060.00180.15010.00560.1884-7.3892-8.91918.3026
20.7446-0.22420.0542.50430.89862.17940.08180.0289-0.0062-0.1901-0.1554-0.0258-0.1625-0.1561-0.01720.1290.04070.01090.18060.0030.1477-8.85168.7455-10.5315
30.6888-0.23290.13010.71190.25570.90020.07060.15850.11040.2917-0.1373-0.1731-0.27950.43330.01720.3186-0.1503-0.0580.24950.05580.21530.35719.723918.3101
40.3890.1687-0.17590.28590.23180.46970.02450.01950.04950.1998-0.03720.0246-0.65080.36970.00270.2857-0.0601-0.02960.22920.02670.2023-2.930310.089619.529
50.66080.47390.29820.86290.03290.1840.2546-0.0569-0.15820.1028-0.0833-0.01490.642-0.0190.05760.41540.0619-0.02710.22460.01890.2326-5.7471-11.2062-10.0617
60.4195-0.19040.33670.39150.17380.51490.21570.0339-0.1472-0.0497-0.1808-0.10450.59160.0041-0.01850.4178-0.042-0.02060.21930.00730.2403-8.2847-12.8783-11.0287
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA2 - 160
2X-RAY DIFFRACTION2chain BB1 - 161
3X-RAY DIFFRACTION3chain CC-4 - 4
4X-RAY DIFFRACTION4chain DD-4 - 4
5X-RAY DIFFRACTION5chain EE-4 - 4
6X-RAY DIFFRACTION6chain FF-4 - 4

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