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- PDB-4qfq: Crystal structure of natvie Npu DnaE split intein -

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Basic information

Entry
Database: PDB / ID: 4qfq
TitleCrystal structure of natvie Npu DnaE split intein
Components
  • DNA polymerase III, alpha subunit
  • Nucleic acid binding, OB-fold, tRNA/helicase-type
KeywordsSPLICING / Split-intein / intein / Protein trans-splicing
Function / homology
Function and homology information


intein-mediated protein splicing / 3'-5' exonuclease activity / helicase activity / DNA replication / nucleic acid binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / metal ion binding
Similarity search - Function
Bacterial DNA polymerase III alpha subunit, thumb domain / DNA polymerase III, alpha subunit / Bacterial DNA polymerase III, alpha subunit, NTPase domain / DNA polymerase, helix-hairpin-helix motif / DNA polymerase III alpha subunit finger domain / Bacterial DNA polymerase III alpha NTPase domain / Helix-hairpin-helix motif / Bacterial DNA polymerase III alpha subunit finger domain / Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain ...Bacterial DNA polymerase III alpha subunit, thumb domain / DNA polymerase III, alpha subunit / Bacterial DNA polymerase III, alpha subunit, NTPase domain / DNA polymerase, helix-hairpin-helix motif / DNA polymerase III alpha subunit finger domain / Bacterial DNA polymerase III alpha NTPase domain / Helix-hairpin-helix motif / Bacterial DNA polymerase III alpha subunit finger domain / Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / PHP domain / PHP domain / Polymerase/histidinol phosphatase, N-terminal / DNA polymerase alpha chain like domain / Polymerase/histidinol phosphatase-like / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Beta Complex / Mainly Beta
Similarity search - Domain/homology
DNA polymerase III, alpha subunit / Nucleic acid binding, OB-fold, tRNA/helicase-type
Similarity search - Component
Biological speciesNostoc punctiforme (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.035 Å
AuthorsLee, Y.Z. / Kuo, J.H. / Sue, S.C.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of natvie Npu DnaE split intein
Authors: Lee, Y.Z. / Kuo, J.H. / Sue, S.C.
History
DepositionMay 21, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 27, 2015Provider: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase III, alpha subunit
B: Nucleic acid binding, OB-fold, tRNA/helicase-type


Theoretical massNumber of molelcules
Total (without water)17,1852
Polymers17,1852
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-27 kcal/mol
Surface area6840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.798, 48.694, 75.686
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA polymerase III, alpha subunit


Mass: 12995.582 Da / Num. of mol.: 1 / Fragment: N fragment, UNP residues 775-876
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc punctiforme (bacteria) / Strain: ATCC 29133 / PCC 73102 / Gene: Npun_F4872 / Production host: Escherichia coli (E. coli) / References: UniProt: B2J066, DNA-directed DNA polymerase
#2: Protein/peptide Nucleic acid binding, OB-fold, tRNA/helicase-type


Mass: 4189.819 Da / Num. of mol.: 1 / Fragment: C fragment, UNP residues 2-36
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc punctiforme (bacteria) / Strain: ATCC 29133 / PCC 73102 / Gene: Npun_F5684 / Production host: Escherichia coli (E. coli) / References: UniProt: B2J821, DNA-directed DNA polymerase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.02 Å3/Da / Density % sol: 34.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: 0.2M ammonium sulfate, 0.1M sodium cacodylate trihydrate, 30% Polyethylene glycol(PEG) 8,000, pH 6.5, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 27, 2013
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.035→26.52 Å / Num. all: 8701 / Num. obs: 8498 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.03-2.1197.39
2.358-2.974199.78
2.974-3.75194.92
3.75-4.727191.64
4.73-5.963199.46
5.966-7.5221100
7.526-9.4861100
9.506-26.517199.01

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NZM

3nzm


Resolution: 2.035→26.517 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 34.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2873 848 10 %RANDOM
Rwork0.2298 ---
obs0.2361 8480 97.46 %-
all-8706 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.035→26.517 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1104 0 0 14 1118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181123
X-RAY DIFFRACTIONf_angle_d1.4121516
X-RAY DIFFRACTIONf_dihedral_angle_d18.351423
X-RAY DIFFRACTIONf_chiral_restr0.118168
X-RAY DIFFRACTIONf_plane_restr0.005197
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.035-2.16250.38571330.2715120195
2.1625-2.32940.35651430.28191272100
2.3294-2.56360.36461420.27621280100
2.5636-2.93420.33871440.25391299100
2.9342-3.69520.28491420.2316128598
3.6952-26.51950.22531440.1936129593
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)
15.34362.57730.12317.0202-2.93062.39840.6147-0.2741-0.03060.3249-0.77260.97970.04060.41830.42990.2285-0.02480.0160.36430.00490.2254.553646.45580.0475
27.7773-0.73341.06784.4393-0.1277.3654-0.1496-0.51180.10720.5108-0.2623-0.0663-0.3797-0.45910.20630.2628-0.02470.00420.38970.08420.16678.646545.639993.5198
33.525-5.26471.23817.9871-0.93498.11390.07491.1152-0.86770.2606-0.48510.66840.2072-0.6953-0.09030.15840.0289-0.01910.471-0.04480.24822.440345.571688.1021
41.7231.19780.43777.5666-0.88597.8893-0.443-0.1895-0.08090.17690.3367-0.0945-1.02440.35230.02850.3188-0.0843-0.0370.6699-0.03410.052612.031854.833793.1851
55.4717-3.1962-3.46575.87291.2022.6614-0.17570.1408-0.0967-0.26110.33350.3457-1.284-0.2919-0.36570.2225-0.00710.04280.53430.05080.26420.14853.952480.5095
65.57070.79792.57978.07650.65224.1241-0.17110.9509-0.5328-0.06090.296-0.2990.42050.8369-0.25530.18880.10770.00020.5628-0.01910.240916.295643.205573.5322
73.65092.32251.70757.53781.65414.0035-0.36860.12020.2964-0.09960.1080.1718-0.03630.0660.04560.17240.02030.02650.33560.0160.127211.813951.377775.8718
89.5637-8.87290.13788.97311.71284.549-0.4030.83961.636-0.0355-0.2661-1.9056-0.8941.3146-0.4720.2966-0.1180.03920.59940.2010.369524.547457.746179.2372
96.1636-1.9628-5.59529.47436.48168.63140.26421.0808-0.0677-0.78080.3281-0.6303-0.152-0.627-0.16660.1885-0.08970.03170.56470.04150.158317.310454.826971.4179
109.10112.1966-5.85239.6508-5.4191.9998-0.0499-0.4094-0.8460.3134-0.4283-0.64610.65741.20960.85110.231-0.0232-0.0440.46770.09830.3923.090949.672181.4199
116.0269-1.62713.91456.2254-3.20614.5745-0.08790.81-1.94120.20820.1496-0.345-0.22690.48870.51340.3570.02760.0550.2382-0.11140.390721.595245.313772.0581
122.0302-1.4541.16223.3251.72811.9993-0.67270.06561.03360.2099-0.1639-0.67730.8474-1.6069-0.71470.1778-0.02380.02350.636-0.040.31538.277344.848266.4589
137.56953.91784.3523.19773.71326.6751-0.81790.49870.2425-0.61510.20860.7535-0.6406-0.19860.16560.31490.0211-0.11450.41280.00830.20352.437952.704481.0171
146.0689-1.2082-1.10032.9948-3.14954.3164-0.5147-0.00360.7591.12230.3662-0.5026-1.1911-0.5031-0.35180.50580.0589-0.08860.1984-0.01130.350712.785658.731888.9146
154.0727-2.24990.9892.0151-2.01663.11560.77481.12130.2371-0.7281-0.9737-0.47220.10591.3614-0.02430.28050.0316-0.02310.50790.02510.196414.782949.558983.967
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 6 )
2X-RAY DIFFRACTION2chain 'A' and (resid 7 through 13 )
3X-RAY DIFFRACTION3chain 'A' and (resid 14 through 23 )
4X-RAY DIFFRACTION4chain 'A' and (resid 24 through 43 )
5X-RAY DIFFRACTION5chain 'A' and (resid 44 through 55 )
6X-RAY DIFFRACTION6chain 'A' and (resid 56 through 64 )
7X-RAY DIFFRACTION7chain 'A' and (resid 65 through 75 )
8X-RAY DIFFRACTION8chain 'A' and (resid 76 through 80 )
9X-RAY DIFFRACTION9chain 'A' and (resid 81 through 89 )
10X-RAY DIFFRACTION10chain 'A' and (resid 90 through 101 )
11X-RAY DIFFRACTION11chain 'B' and (resid 103 through 107 )
12X-RAY DIFFRACTION12chain 'B' and (resid 108 through 112 )
13X-RAY DIFFRACTION13chain 'B' and (resid 113 through 122 )
14X-RAY DIFFRACTION14chain 'B' and (resid 123 through 128 )
15X-RAY DIFFRACTION15chain 'B' and (resid 129 through 137 )

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