[English] 日本語
Yorodumi
- PDB-4qfq: Crystal structure of natvie Npu DnaE split intein -

+
Open data


ID or keywords:

Loading...

-
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
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 / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / Hint domain superfamily / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more