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- PDB-5oxw: Structure of NeqN from Nanoarchaeum equitans -

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Basic information

Entry
Database: PDB / ID: 5oxw
TitleStructure of NeqN from Nanoarchaeum equitans
Components
  • ALA-SER-GLY-SER-PHE-LYS-VAL-ILE-TYR-GLY-ASP
  • NEQ068
KeywordsSPLICING / Intein complex
Function / homology
Function and homology information


nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / base-excision repair, gap-filling / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding
Similarity search - Function
DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
DNA-directed DNA polymerase
Similarity search - Component
Biological speciesNanoarchaeum equitans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.61 Å
AuthorsAparicio, D. / Perez-Luque, R. / Ribo, M. / Fita, I.
CitationJournal: Cell Chem Biol / Year: 2018
Title: Structural Insights into Subunits Assembly and the Oxyester Splicing Mechanism of Neq pol Split Intein.
Authors: Gordo, V. / Aparicio, D. / Perez-Luque, R. / Benito, A. / Vilanova, M. / Uson, I. / Fita, I. / Ribo, M.
History
DepositionSep 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title
Revision 1.2May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEQ068
B: NEQ068
C: NEQ068
D: NEQ068
E: ALA-SER-GLY-SER-PHE-LYS-VAL-ILE-TYR-GLY-ASP
F: ALA-SER-GLY-SER-PHE-LYS-VAL-ILE-TYR-GLY-ASP
G: ALA-SER-GLY-SER-PHE-LYS-VAL-ILE-TYR-GLY-ASP
H: ALA-SER-GLY-SER-PHE-LYS-VAL-ILE-TYR-GLY-ASP


Theoretical massNumber of molelcules
Total (without water)50,5498
Polymers50,5498
Non-polymers00
Water1267
1
A: NEQ068
H: ALA-SER-GLY-SER-PHE-LYS-VAL-ILE-TYR-GLY-ASP


Theoretical massNumber of molelcules
Total (without water)12,6372
Polymers12,6372
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NEQ068
E: ALA-SER-GLY-SER-PHE-LYS-VAL-ILE-TYR-GLY-ASP


Theoretical massNumber of molelcules
Total (without water)12,6372
Polymers12,6372
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: NEQ068
F: ALA-SER-GLY-SER-PHE-LYS-VAL-ILE-TYR-GLY-ASP


Theoretical massNumber of molelcules
Total (without water)12,6372
Polymers12,6372
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: NEQ068
G: ALA-SER-GLY-SER-PHE-LYS-VAL-ILE-TYR-GLY-ASP


Theoretical massNumber of molelcules
Total (without water)12,6372
Polymers12,6372
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.930, 67.720, 77.840
Angle α, β, γ (deg.)90.00, 129.91, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13E
23H
14F
24G

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A7 - 77
2112B7 - 77
1122C7 - 86
2122D7 - 86
1132E194 - 204
2132H194 - 204
1142F194 - 204
2142G194 - 204

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.984878, 0.005128, -0.173172), (-0.00358, 0.999951, 0.009249), (0.173211, -0.008489, 0.984848)-23.874, 1.54281, 15.7279

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Components

#1: Protein
NEQ068


Mass: 11492.942 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nanoarchaeum equitans (strain Kin4-M) (archaea)
Gene: NEQ068 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q74N74
#2: Protein/peptide
ALA-SER-GLY-SER-PHE-LYS-VAL-ILE-TYR-GLY-ASP


Mass: 1144.256 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nanoarchaeum equitans (archaea) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.2 Å3/Da / Density % sol: 44.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.1M Di-ammonium Tartrate pH7

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.1478 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1478 Å / Relative weight: 1
ReflectionResolution: 2.61→51.01 Å / Num. all: 40134 / Num. obs: 13172 / % possible obs: 97.9 % / Redundancy: 3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.038 / Rrim(I) all: 0.054 / Net I/σ(I): 16.4
Reflection shellResolution: 2.61→2.68 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.8 / Num. unique all: 3061 / Num. unique obs: 970 / CC1/2: 0.72 / Rpim(I) all: 0.599 / Rrim(I) all: 0.871 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.61→51.01 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / SU B: 30.681 / SU ML: 0.285 / Cross valid method: THROUGHOUT / ESU R: 0.859 / ESU R Free: 0.327 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2574 581 4.4 %RANDOM
Rwork0.20799 ---
obs0.21013 12591 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 81.396 Å2
Baniso -1Baniso -2Baniso -3
1-2.6 Å2-0 Å22.17 Å2
2---6.88 Å2-0 Å2
3---0.27 Å2
Refinement stepCycle: 1 / Resolution: 2.61→51.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2814 0 0 7 2821
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192913
X-RAY DIFFRACTIONr_bond_other_d0.0050.022689
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.9553929
X-RAY DIFFRACTIONr_angle_other_deg0.92236261
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.875347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.60724.853136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.11215512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.127154
X-RAY DIFFRACTIONr_chiral_restr0.0770.2415
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023205
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02607
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_it2.1926.1881400
X-RAY DIFFRACTIONr_mcbond_other2.1926.1841399
X-RAY DIFFRACTIONr_mcangle_it3.8039.2441743
X-RAY DIFFRACTIONr_mcangle_other3.8039.2481744
X-RAY DIFFRACTIONr_scbond_it2.016.3511513
X-RAY DIFFRACTIONr_scbond_other2.0086.3421511
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4459.4322186
X-RAY DIFFRACTIONr_long_range_B_refined5.93665.0932953
X-RAY DIFFRACTIONr_long_range_B_other5.93565.1262954
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A735medium positional0.030.5
22B813medium positional0.020.5
33C91medium positional0.030.5
44D91medium positional0.020.5
11A425tight thermal2.640.5
22B478tight thermal2.590.5
33C64tight thermal6.360.5
44D64tight thermal4.250.5
11A735medium thermal2.862
22B813medium thermal2.522
33C91medium thermal6.712
44D91medium thermal4.142
LS refinement shellResolution: 2.61→2.678 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.464 48 -
Rwork0.327 916 -
obs--98.57 %
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)
11.4027-0.06631.60312.077-0.39253.5510.1713-0.38670.05731.3913-0.20430.49390.1798-0.29910.03310.2259-0.08010.10960.1234-0.03580.071254.898418.718538.5654
22.8797-0.38051.069611.9739-1.35863.7230.0652-0.3046-0.13851.1738-0.01780.27720.1605-0.0531-0.04740.1662-0.03130.05260.0531-0.00980.041181.472417.41389.0163
32.17950.438-0.40559.49310.50715.0850.14950.50190.043-1.1128-0.15050.4923-0.1061-0.06490.00090.15170.0709-0.04410.13680.02440.079979.365117.2863-11.3283
42.7240.6023-0.584810.34991.83884.33960.18130.35470.0586-1.4201-0.27070.3454-0.2776-0.02520.08940.22580.0791-0.03840.06650.00740.060156.510818.602818.1332
51.4770.31990.306812.632311.216912.56430.1627-0.05860.10540.8393-0.18420.57190.3881-0.19320.02150.1215-0.0320.10810.1552-0.00070.223871.268115.01517.5843
64.01351.33682.143210.57175.59729.58470.2641-0.01620.0392-0.4874-0.28790.91090.1962-0.58140.02380.08050.0159-0.10390.1104-0.03260.223870.099420.245-9.3746
70.60552.12481.193311.41083.52972.4921-0.1430.08330.0699-0.56460.03850.5752-0.31040.15410.10440.0990.041-0.10370.2728-0.04640.265246.990521.879319.1592
81.38995.09385.916127.979125.352126.65220.2352-0.1194-0.18741.21990.05080.75081.1158-0.3172-0.28590.0853-0.01920.10030.2731-0.07470.499545.471216.089635.6577
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 76
2X-RAY DIFFRACTION2B7 - 76
3X-RAY DIFFRACTION3C7 - 85
4X-RAY DIFFRACTION4D7 - 85
5X-RAY DIFFRACTION5E-11 - -1
6X-RAY DIFFRACTION6F-11 - -1
7X-RAY DIFFRACTION7G-11 - -1
8X-RAY DIFFRACTION8H-11 - -1

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