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- PDB-2dvy: Crystal structure of restriction endonucleases PabI -

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Basic information

Entry
Database: PDB / ID: 2dvy
TitleCrystal structure of restriction endonucleases PabI
ComponentsRestriction endonuclease PabI
KeywordsHYDROLASE / Restriction endonuclease
Function / homologyRestriction endonuclease, type II, Pab1 / R.Pab1 restriction endonuclease / Restriction endonuclease type II Pab1 domain-containing protein
Function and homology information
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsMiyazono, K. / Watanabe, M. / Kamo, M. / Sawasaki, T. / Nagata, K. / Endo, Y. / Tanokura, M. / Kobayashi, I.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: Novel protein fold discovered in the PabI family of restriction enzymes
Authors: Miyazono, K. / Watanabe, M. / Kosinski, J. / Ishikawa, K. / Kamo, M. / Sawasaki, T. / Nagata, K. / Bujnicki, J.M. / Endo, Y. / Tanokura, M. / Kobayashi, I.
History
DepositionAug 1, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Mar 13, 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 PabI
B: Restriction endonuclease PabI
C: Restriction endonuclease PabI
D: Restriction endonuclease PabI
E: Restriction endonuclease PabI
F: Restriction endonuclease PabI


Theoretical massNumber of molelcules
Total (without water)156,3006
Polymers156,3006
Non-polymers00
Water0
1
A: Restriction endonuclease PabI
B: Restriction endonuclease PabI


Theoretical massNumber of molelcules
Total (without water)52,1002
Polymers52,1002
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-21 kcal/mol
Surface area22230 Å2
MethodPISA
2
C: Restriction endonuclease PabI
D: Restriction endonuclease PabI


Theoretical massNumber of molelcules
Total (without water)52,1002
Polymers52,1002
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-17 kcal/mol
Surface area21850 Å2
MethodPISA
3
E: Restriction endonuclease PabI
F: Restriction endonuclease PabI


Theoretical massNumber of molelcules
Total (without water)52,1002
Polymers52,1002
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-20 kcal/mol
Surface area21820 Å2
MethodPISA
4
A: Restriction endonuclease PabI
B: Restriction endonuclease PabI
C: Restriction endonuclease PabI
D: Restriction endonuclease PabI


Theoretical massNumber of molelcules
Total (without water)104,2004
Polymers104,2004
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9340 Å2
ΔGint-42 kcal/mol
Surface area41190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.570, 113.956, 89.173
Angle α, β, γ (deg.)90.00, 116.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Restriction endonuclease PabI


Mass: 26050.012 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea)
Description: wheat-germ-based cell-free protein synthesis system
References: UniProt: Q9V2B6

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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: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 5% PEG 6000, 0.1M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 7.5 % / Av σ(I) over netI: 17.8 / Number: 251759 / Rmerge(I) obs: 0.077 / Χ2: 2.6 / D res high: 2.9 Å / D res low: 20 Å / Num. obs: 33524 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.192099.810.0546.0987.3
4.946.1910010.0634.0197.5
4.324.9410010.0643.6857.5
3.934.3210010.0732.9937.5
3.653.9310010.092.3987.5
3.443.6510010.1031.9977.6
3.263.4410010.1231.6697.6
3.123.2610010.1621.2997.6
33.1210010.2211.0497.6
2.9310010.280.9047.6
ReflectionResolution: 3→20 Å / Num. obs: 30368 / % possible obs: 99.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.067 / Χ2: 1.766 / Net I/σ(I): 14.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3-3.113.40.28329271.08296.7
3.11-3.233.50.21130051.13698.2
3.23-3.383.50.15230041.31599.2
3.38-3.553.60.11130611.47899.9
3.55-3.783.60.10630112.00699.9
3.78-4.063.60.08130771.87499.9
4.06-4.473.60.0630492.2599.9
4.47-5.113.50.05330362.41699.9
5.11-6.43.80.05130942.081100
6.4-203.80.03531041.8799.8

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Phasing

PhasingMethod: SAD
Phasing MAD set
IDHighest resolution (Å)Lowest resolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_12.919.8900324851112
ANO_12.919.891.4070324730
Phasing MAD set shell
IDResolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_110.95-19.890048855
ISO_18.4-10.950071555
ISO_17.07-8.40088855
ISO_16.23-7.0700103251
ISO_15.62-6.2300112649
ISO_15.17-5.6200126448
ISO_14.81-5.1700137957
ISO_14.51-4.8100146050
ISO_14.27-4.5100153349
ISO_14.06-4.2700167758
ISO_13.88-4.0600176855
ISO_13.72-3.8800185153
ISO_13.58-3.7200191358
ISO_13.45-3.5800200856
ISO_13.34-3.4500206760
ISO_13.23-3.3400211961
ISO_13.14-3.2300220659
ISO_13.05-3.1400226062
ISO_12.97-3.0500232658
ISO_12.9-2.9700240563
ANO_110.95-19.894.2604830
ANO_18.4-10.953.40907130
ANO_17.07-8.43.48608850
ANO_16.23-7.073.329010310
ANO_15.62-6.232.948011250
ANO_15.17-5.622.656012640
ANO_14.81-5.172.313013790
ANO_14.51-4.812.003014600
ANO_14.27-4.511.738015330
ANO_14.06-4.271.471016770
ANO_13.88-4.061.209017680
ANO_13.72-3.881.008018510
ANO_13.58-3.720.882019130
ANO_13.45-3.580.727020080
ANO_13.34-3.450.616020670
ANO_13.23-3.340.512021190
ANO_13.14-3.230.451022060
ANO_13.05-3.140.379022600
ANO_12.97-3.050.327023260
ANO_12.9-2.970.3024050
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
1-16.22877.23766.206SE84.660.83
2-18.17150.72678.92SE86.40.8
3-10.67740.49345.48SE85.080.71
4-19.01876.79470.878SE77.140.7
5-16.997109.82179.821SE79.90.65
622.23357.43877.989SE81.320.62
723.40994.08442.767SE90.410.67
837.65210.69260.091SE82.950.54
9-8.54344.47342.537SE81.510.6
10-20.74355.05476.933SE79.490.62
1133.7026.93658.762SE91.750.64
1259.03734.24248.079SE130.10.51
13-21.8733.82778.321SE120.010.47
14-6.88320.59973.708SE100.620.4
1529.02494.49542.251SE88.120.52
1649.98317.59852.001SE118.720.47

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS1.1refinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 3→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1513632.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.318 3044 10 %RANDOM
Rwork0.247 ---
all0.247 ---
obs0.247 30318 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.2274 Å2 / ksol: 0.308197 e/Å3
Displacement parametersBiso mean: 66.5 Å2
Baniso -1Baniso -2Baniso -3
1-5.63 Å20 Å216.84 Å2
2---1.41 Å20 Å2
3----4.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10623 0 0 0 10623
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.406 519 10.3 %
Rwork0.342 4500 -
obs-5019 99.4 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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