[English] 日本語
Yorodumi
- PDB-7bmf: Crystal structure of RecJCdc45 from Methanothermobacter thermoaut... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7bmf
TitleCrystal structure of RecJCdc45 from Methanothermobacter thermoautotroficus in complex with dCTP
ComponentsConserved proteinConservation
KeywordsDNA BINDING PROTEIN / Phosphodiesterase
Function / homology
Function and homology information


exonuclease activity / nucleic acid binding / nucleotide binding / metal ion binding
Similarity search - Function
: / DHH-CID domain / DDH domain / DHH family / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain
Similarity search - Domain/homology
CYTIDINE-5'-TRIPHOSPHATE / : / NITRATE ION / DI(HYDROXYETHYL)ETHER / Single-stranded-DNA-specific exonuclease RecJ
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDe March, M. / Onesti, S.
CitationJournal: To Be Published
Title: Crystal structure of RecJCdc45 from Methanothermobacter thermoautotroficus
Authors: De March, M. / Onesti, S.
History
DepositionJan 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Conserved protein
B: Conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,53219
Polymers101,4432
Non-polymers2,08917
Water3,711206
1
A: Conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,88111
Polymers50,7211
Non-polymers1,15910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6518
Polymers50,7211
Non-polymers9297
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.750, 53.880, 86.720
Angle α, β, γ (deg.)79.860, 82.770, 63.980
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Conserved protein / Conservation / phosphodiesterase


Mass: 50721.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) (archaea)
Strain: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H
Gene: MTH_1422 / Production host: Escherichia coli (E. coli) / References: UniProt: O27473

-
Non-polymers , 5 types, 223 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate


Mass: 483.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O14P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: NO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M bis-Tris propane pH 6.5, 14% w/v PEG 3350, 0.2M sodium nitrate, 1mM MnCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→48.23 Å / Num. obs: 42571 / % possible obs: 97.6 % / Redundancy: 2 % / CC1/2: 0.942 / Net I/σ(I): 3.4
Reflection shellResolution: 2.2→2.27 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 3602 / CC1/2: 0.831

-
Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TVV

6tvv


Resolution: 2.2→42.21 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.852 / SU B: 7.549 / SU ML: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.274 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2991 2785 5.1 %RANDOM
Rwork0.2535 ---
obs0.2558 42570 94.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.79 Å2 / Biso mean: 30.87 Å2 / Biso min: 8.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0.01 Å20.16 Å2
2--0.09 Å2-0.01 Å2
3----0.13 Å2
Refinement stepCycle: final / Resolution: 2.2→42.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6491 0 102 206 6799
Biso mean--37.61 30.92 -
Num. residues----888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0196687
X-RAY DIFFRACTIONr_bond_other_d0.0020.026246
X-RAY DIFFRACTIONr_angle_refined_deg1.8051.9859060
X-RAY DIFFRACTIONr_angle_other_deg1.124314288
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5315886
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0523.783267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.494151020
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0471544
X-RAY DIFFRACTIONr_chiral_restr0.1260.21048
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027702
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021472
LS refinement shellResolution: 2.21→2.27 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.349 186 -
Rwork0.324 3289 -
obs--82.02 %

+
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