[English] 日本語
Yorodumi
- PDB-4drf: Crystal Structure of Bacterial Pnkp-C/Hen1-N Heterodimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4drf
TitleCrystal Structure of Bacterial Pnkp-C/Hen1-N Heterodimer
Components
  • Metallophosphoesterase
  • Methyltransferase type 12
KeywordsPROTEIN BINDING / TRANSFERASE / RNA repair / RNA ligase / Ligase-activating
Function / homology
Function and homology information


small RNA 2'-O-methyltransferase / RNA methyltransferase activity / RNA methylation / O-methyltransferase activity / S-adenosylmethionine-dependent methyltransferase activity / hydrolase activity / carbohydrate metabolic process / GTP binding / ATP binding / identical protein binding / metal ion binding
Similarity search - Function
Hen1, N-terminal domain / Helix Hairpins - #1010 / : / 3'-RNA ribose 2'-O-methyltransferase, Hen1, bacterial / Hen1, N-terminal / Hen1, N-terminal domain superfamily / RNA repair, ligase-Pnkp-associating, region of Hen1 / 3'-RNA ribose 2'-O-methyltransferase, Hen1 / c-terminal autoproteolytic domain of nucleoporin nup98 / Polynucleotide kinase-phosphatase, bacterial ...Hen1, N-terminal domain / Helix Hairpins - #1010 / : / 3'-RNA ribose 2'-O-methyltransferase, Hen1, bacterial / Hen1, N-terminal / Hen1, N-terminal domain superfamily / RNA repair, ligase-Pnkp-associating, region of Hen1 / 3'-RNA ribose 2'-O-methyltransferase, Hen1 / c-terminal autoproteolytic domain of nucleoporin nup98 / Polynucleotide kinase-phosphatase, bacterial / PrpE-like, metallophosphatase domain / Polynucleotide kinase-phosphatase, ligase domain / PNKP adenylyltransferase domain, ligase domain / AAA domain / DNA ligase/mRNA capping enzyme / Methyltransferase type 12 / Methyltransferase domain / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Helix Hairpins / Metallo-dependent phosphatase-like / D-amino Acid Aminotransferase; Chain A, domain 1 / Helix non-globular / Special / S-adenosyl-L-methionine-dependent methyltransferase superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Small RNA 2'-O-methyltransferase / Metallophosphoesterase
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHuang, R.H. / Wang, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Molecular basis of bacterial protein Hen1 activating the ligase activity of bacterial protein Pnkp for RNA repair.
Authors: Wang, P. / Chan, C.M. / Christensen, D. / Zhang, C. / Selvadurai, K. / Huang, R.H.
History
DepositionFeb 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Database references
Revision 1.2Aug 29, 2012Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Metallophosphoesterase
B: Methyltransferase type 12
C: Metallophosphoesterase
D: Methyltransferase type 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,3315
Polymers150,2394
Non-polymers921
Water2,774154
1
A: Metallophosphoesterase
B: Methyltransferase type 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2113
Polymers75,1192
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-29 kcal/mol
Surface area26000 Å2
MethodPISA
2
C: Metallophosphoesterase
D: Methyltransferase type 12


Theoretical massNumber of molelcules
Total (without water)75,1192
Polymers75,1192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-27 kcal/mol
Surface area25950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.667, 59.707, 101.542
Angle α, β, γ (deg.)81.27, 87.67, 88.39
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 452:648 OR RESSEQ 660:870 )
211CHAIN C AND (RESSEQ 452:648 OR RESSEQ 660:870 )
112CHAIN B AND (RESSEQ 1:61 OR RESSEQ 73:196 OR RESSEQ 203:223 )
212CHAIN D AND (RESSEQ 1:61 OR RESSEQ 73:196 OR RESSEQ 203:223 )

NCS ensembles :
ID
1
2

-
Components

#1: Protein Metallophosphoesterase


Mass: 48882.141 Da / Num. of mol.: 2 / Fragment: C-terminal half of bacterial Pnkp
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: ATCC 27405 / DSM 1237 / Gene: Cthe_2768 / Production host: Escherichia coli (E. coli) / References: UniProt: A3DJ38
#2: Protein Methyltransferase type 12


Mass: 26237.260 Da / Num. of mol.: 2 / Fragment: N-terminal half of bacterial Hen1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: ATCC 27405 / DSM 1237 / Gene: Cthe_2767 / Production host: Escherichia coli (E. coli) / References: UniProt: A3DJ37
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.38 Å3/Da / Density % sol: 48.26 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7.75
Details: 16% PEG6000, 0.5M NaCl, 25mM CaCl2, 5% methanol, 50mM HEPES, 50 mM Tris-HCl, pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 303K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 34296 / Num. obs: 41067 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

-
Processing

Software
NameClassification
MAR345dtbdata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→42.404 Å / SU ML: 0.42 / σ(F): 0.16 / Phase error: 27.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2446 1978 4.82 %Random
Rwork0.1845 ---
obs0.1874 33610 96.22 %-
all-42680 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.928 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.8585 Å2-10.1317 Å2-2.3552 Å2
2---2.1152 Å21.1218 Å2
3---7.9737 Å2
Refinement stepCycle: LAST / Resolution: 2.6→42.404 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9886 0 6 154 10046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110111
X-RAY DIFFRACTIONf_angle_d1.28413657
X-RAY DIFFRACTIONf_dihedral_angle_d16.233808
X-RAY DIFFRACTIONf_chiral_restr0.0851496
X-RAY DIFFRACTIONf_plane_restr0.0061736
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3276X-RAY DIFFRACTIONPOSITIONAL
12C3276X-RAY DIFFRACTIONPOSITIONAL0.053
21B1667X-RAY DIFFRACTIONPOSITIONAL
22D1667X-RAY DIFFRACTIONPOSITIONAL0.055
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6610.39341270.27352449X-RAY DIFFRACTION87
2.661-2.73290.32041380.24362641X-RAY DIFFRACTION91
2.7329-2.81330.34141360.25612698X-RAY DIFFRACTION93
2.8133-2.90410.35241330.21142729X-RAY DIFFRACTION95
2.9041-3.00790.30441460.22472822X-RAY DIFFRACTION96
3.0079-3.12830.29041360.19412807X-RAY DIFFRACTION97
3.1283-3.27060.2991480.212816X-RAY DIFFRACTION98
3.2706-3.4430.27721440.20212844X-RAY DIFFRACTION98
3.443-3.65860.24071470.18622881X-RAY DIFFRACTION99
3.6586-3.94090.20361430.17382866X-RAY DIFFRACTION99
3.9409-4.33710.21981450.15662885X-RAY DIFFRACTION99
4.3371-4.96380.19911500.13422906X-RAY DIFFRACTION99
4.9638-6.25070.19161460.17612871X-RAY DIFFRACTION99
6.2507-42.41010.2071390.17872874X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -14.2422 Å / Origin y: -28.7383 Å / Origin z: 37.5273 Å
111213212223313233
T0.1566 Å20.0319 Å2-0.0073 Å2-0.1329 Å2-0.0023 Å2--0.1697 Å2
L0.1955 °20.1486 °2-0.0377 °2-0.0831 °2-0.0341 °2--0.0826 °2
S0.013 Å °-0.0358 Å °0.0269 Å °0.005 Å °-0.0087 Å °-0.0073 Å °0.017 Å °0.0028 Å °-0 Å °
Refinement TLS groupSelection details: ALL

+
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