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- PDB-5gkk: Crystal structure of a homing endonuclease, I-TnaI -

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Basic information

Entry
Database: PDB / ID: 5gkk
TitleCrystal structure of a homing endonuclease, I-TnaI
ComponentsPutative homing endonuclease
KeywordsHYDROLASE / Homing endonuclease / Maturase
Function / homologyLAGLIDADG endonuclease / Homing endonuclease, LAGLIDADG / Homing endonuclease / endonuclease activity / Putative homing endonuclease
Function and homology information
Biological speciesThermotoga neapolitana (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsRen, J.
CitationJournal: To Be Published
Title: Crystal structure of a homing endonuclease, I-TnaI
Authors: Ren, J.
History
DepositionJul 4, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative homing endonuclease
B: Putative homing endonuclease


Theoretical massNumber of molelcules
Total (without water)40,7722
Polymers40,7722
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-9 kcal/mol
Surface area15290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.203, 113.886, 44.922
Angle α, β, γ (deg.)90.000, 110.410, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative homing endonuclease


Mass: 20385.818 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga neapolitana (bacteria) / Strain: DSM 4359 / Gene: i-Tna1931b / Production host: Escherichia coli (E. coli) / References: UniProt: Q70PR2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 1.89 Å3/Da / Density % sol: 35.04 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 100 mM Hepes, 35% Jeffamine ED-2001

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.54175 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54175 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 19699 / % possible obs: 96.5 % / Redundancy: 6.2 % / Biso Wilson estimate: 37.3 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 16.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.719 / Mean I/σ(I) obs: 4.3 / % possible all: 96

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data processing
HKL-2000data scaling
PHASERphasing
PHENIX1.7.3_928refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BP7

1bp7


Resolution: 2.001→39.49 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 28.68
RfactorNum. reflection% reflectionSelection details
Rfree0.2479 995 5.06 %Random
Rwork0.2047 ---
obs0.2071 19667 96.16 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Bsol: 46.95 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso max: 106.41 Å2 / Biso mean: 46.5213 Å2 / Biso min: 23.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.7089 Å20 Å2-3.3439 Å2
2--10.0693 Å20 Å2
3----7.3604 Å2
Refinement stepCycle: LAST / Resolution: 2.001→39.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2450 0 0 31 2481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012494
X-RAY DIFFRACTIONf_angle_d1.2753316
X-RAY DIFFRACTIONf_chiral_restr0.096353
X-RAY DIFFRACTIONf_plane_restr0.005417
X-RAY DIFFRACTIONf_dihedral_angle_d17.438996
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0011-2.10660.35461370.24992592272994
2.1066-2.23850.28151280.21882672280096
2.2385-2.41140.29511270.20842672279996
2.4114-2.6540.27171400.22542695283597
2.654-3.03790.27361560.21052695285198
3.0379-3.82690.24511380.20142726286498
3.8269-39.49790.21661690.19272620278995
Refinement TLS params.

S33: -0 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.90980.2573-0.79350.1994-0.41331.4956-0.11290.0045-0.0829-0.03950.01130.02780.14-0.04650.31160.01-0.00350.2801-0.00050.282329.0037-7.44326.8368
20.7183-0.52340.57451.3244-0.60410.68680.0121-0.04320.130.0464-0.08710.0532-0.0863-0.00570.2676-0.01740.01210.3034-0.02010.315431.324119.7066-11.6217
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:147)A1 - 147
2X-RAY DIFFRACTION2chain 'B' and (resseq 1:147)B1 - 147

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