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- PDB-3uvf: Expanding LAGALIDADG endonuclease scaffold diversity by rapidly s... -

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Basic information

Entry
Database: PDB / ID: 3uvf
TitleExpanding LAGALIDADG endonuclease scaffold diversity by rapidly surveying evolutionary sequence space
Components
  • (synthetic oligo) x 2
  • Intron-encoded DNA endonuclease I-HjeMI
KeywordsHYDROLASE/DNA / LAGLIDAGD endonuclease / Hydrolase / Divalent metal ions / HYDROLASE-DNA complex
Function / homologyHoming endonucleases / Endonuclease I-creI / Roll / Alpha Beta / DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10)
Function and homology information
Biological speciesTrichoderma reesei (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsJacoby, K. / Metzger, M. / Shen, B. / Jarjour, J. / Stoddard, B. / Scharenberg, A.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Expanding LAGLIDADG endonuclease scaffold diversity by rapidly surveying evolutionary sequence space.
Authors: Jacoby, K. / Metzger, M. / Shen, B.W. / Certo, M.T. / Jarjour, J. / Stoddard, B.L. / Scharenberg, A.M.
History
DepositionNov 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Database references
Revision 1.2Jul 18, 2012Group: Structure summary
Revision 1.3Aug 1, 2012Group: Structure summary
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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: Intron-encoded DNA endonuclease I-HjeMI
C: synthetic oligo
D: synthetic oligo
B: Intron-encoded DNA endonuclease I-HjeMI
E: synthetic oligo
F: synthetic oligo
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,45718
Polymers93,6736
Non-polymers78412
Water3,135174
1
A: Intron-encoded DNA endonuclease I-HjeMI
C: synthetic oligo
D: synthetic oligo
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0637
Polymers46,8363
Non-polymers2264
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8450 Å2
ΔGint-99 kcal/mol
Surface area18400 Å2
MethodPISA
2
B: Intron-encoded DNA endonuclease I-HjeMI
E: synthetic oligo
F: synthetic oligo
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,39411
Polymers46,8363
Non-polymers5588
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8890 Å2
ΔGint-86 kcal/mol
Surface area18760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.591, 73.592, 82.031
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11E-503-

PEG

Detailsmonomer

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Intron-encoded DNA endonuclease I-HjeMI / COB intron protein / mRNA maturase bI1 / Truncated non-functional cytochrome b / DNA ...COB intron protein / mRNA maturase bI1 / Truncated non-functional cytochrome b / DNA endonuclease/RNA maturase I-AniI


Mass: 29624.334 Da / Num. of mol.: 2 / Fragment: I-HjeMI / Mutation: L232K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoderma reesei (fungus) / Gene: I-AniI / Plasmid: pET15b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): RIL+ / References: Hydrolases; Acting on ester bonds

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DNA chain , 2 types, 4 molecules CEDF

#2: DNA chain synthetic oligo


Mass: 8692.586 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic oligo
#3: DNA chain synthetic oligo


Mass: 8519.508 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic oligo

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Non-polymers , 5 types, 186 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.93 Å3/Da / Density % sol: 57.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 3350, 0.2 M Ammonium sulfate, 0.1 M Bis-Tris pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
PH range: pH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 4, 2011 / Details: Si(220), asymmetric curved crystal
RadiationMonochromator: Rh/Pt coated mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→48.71 Å / Num. all: 22753 / Num. obs: 22602 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rsym value: 0.066 / Net I/σ(I): 23.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.49-2.585.30.2515.45193.7
2.58-2.686.10.2167.36194.6
2.68-2.86.30.16610196.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3EH8

3eh8


Resolution: 3→48.71 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.757 / SU B: 67.219 / SU ML: 0.568 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.646 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.37811 1155 5.1 %RANDOM
Rwork0.27974 ---
obs0.28488 21446 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.954 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 3→48.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4182 2284 40 174 6680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226863
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0042.3949725
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.965510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67523.968189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.36215829
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3051521
X-RAY DIFFRACTIONr_chiral_restr0.1030.21083
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024297
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it01.52537
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it024114
X-RAY DIFFRACTIONr_scbond_it034326
X-RAY DIFFRACTIONr_scangle_it04.55610
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.528 82 -
Rwork0.319 1542 -
obs--97.25 %
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)
14.13950.5273-0.872.23080.06350.73580.0319-0.0884-0.068-0.1017-0.057-0.50430.04210.07020.02520.30250.00750.03910.42990.04750.7278-36.8817.856-43.568
24.38450.43561.11351.0950.40491.26870.04020.05260.1206-0.0448-0.0172-0.1394-0.0033-0.1039-0.0230.6713-0.02320.02790.7669-0.00830.99-21.96918.909-83.976
36.32920.2217-0.71461.6220.03071.02980.1071-0.6793-0.1460.1107-0.0381-0.43040.02710.1262-0.0690.3645-0.0048-0.00170.51280.0030.8129-37.21320.565-32.97
48.23430.078-0.97242.26250.15370.69740.0461-0.43050.39620.0944-0.0062-0.3148-0.0738-0.0285-0.03980.3583-0.0076-0.00190.52680.05440.6996-39.5820.875-33.307
58.7338-0.2744-0.19950.76390.02670.6178-0.2133-0.68760.32830.03430.0381-0.20280.0811-0.20120.17520.78150.00610.04760.8765-0.04250.9992-21.36116.197-73.588
68.4639-0.23470.08160.0892-0.15630.2957-0.0592-0.4637-0.4104-0.03710.0113-0.04670.04230.06510.04790.69520.03310.04510.9708-0.05641.2551-19.03315.886-74.033
70.3539-0.0041-0.26590.02080.04480.4186-0.02120.00420.06140.00020.0756-0.01540.09450.0003-0.05440.34390.03570.01390.48350.02520.6687-23.52919.081-61.882
88.0499-2.3141-10.606112.65130.459814.9546-0.0778-0.7693-0.1194-1.4733-0.2508-0.04310.16960.51650.32860.36220.2139-0.24221.14580.01850.41551.3714.902-80.06
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 256
2X-RAY DIFFRACTION1A301 - 303
3X-RAY DIFFRACTION2B2 - 256
4X-RAY DIFFRACTION2B301
5X-RAY DIFFRACTION2E501 - 502
6X-RAY DIFFRACTION3C401 - 428
7X-RAY DIFFRACTION4D501 - 528
8X-RAY DIFFRACTION5E401 - 428
9X-RAY DIFFRACTION6F501 - 528
10X-RAY DIFFRACTION7C501 - 526
11X-RAY DIFFRACTION7E601 - 626
12X-RAY DIFFRACTION7A401 - 443
13X-RAY DIFFRACTION7B401 - 444
14X-RAY DIFFRACTION7D601 - 609
15X-RAY DIFFRACTION7F701 - 726
16X-RAY DIFFRACTION8A304
17X-RAY DIFFRACTION8B302 - 304
18X-RAY DIFFRACTION8E503
19X-RAY DIFFRACTION8F601

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