[English] 日本語
Yorodumi
- PDB-8j4w: Structure of Mycobacterium thermoresistibile NrdI(reduced) determ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8j4w
TitleStructure of Mycobacterium thermoresistibile NrdI(reduced) determined at 1.1 angstrom resolution
ComponentsProtein NrdI
KeywordsFLAVOPROTEIN / Ribonucleotide reductase accessory protein. Metal cofactor assembly
Function / homology
Function and homology information


Ribonucleotide reductase, class Ib, NrdI, bacterial / Ribonucleotide reductase Class Ib, NrdI / NrdI Flavodoxin like / Flavoprotein-like superfamily
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / HYDROGEN PEROXIDE / PEROXIDE ION / SULFITE ION / Protein NrdI
Similarity search - Component
Biological speciesMycolicibacterium thermoresistibile ATCC 19527 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsYadav, L.R. / Mande, S.C.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)DST-NPDF (PDF/2015/000961) and DBT-Centre of Excellence Grant (BT/PR15450/COE/34/46/2016). India
CitationJournal: Curr Res Struct Biol / Year: 2024
Title: Structural insights into the initiation of free radical formation in the Class Ib ribonucleotide reductases in Mycobacteria.
Authors: Yadav, L.R. / Sharma, V. / Shanmugam, M. / Mande, S.C.
History
DepositionApr 21, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Protein NrdI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0806
Polymers16,4431
Non-polymers6385
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Monomer prottein
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-7 kcal/mol
Surface area8200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.737, 36.840, 48.371
Angle α, β, γ (deg.)90.000, 111.530, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

-
Protein , 1 types, 1 molecules C

#1: Protein Protein NrdI


Mass: 16442.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Ribonucleotide reductase cofactor assembly protein
Source: (gene. exp.) Mycolicibacterium thermoresistibile ATCC 19527 (bacteria)
Strain: ATCC 19527 / Gene: nrdI / Plasmid: pET32a+ / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2 (DE3) / References: UniProt: G7CEK1

-
Non-polymers , 6 types, 164 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3
#4: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2
#5: Chemical ChemComp-PER / PEROXIDE ION


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 31.72 % / Description: Rectangular crystals
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.15M potassium phosphate monobasic and 18% PEG 3350. For reduction crystals are soaked in sodium dithionite solution
PH range: 7.5-8.2 / Temp details: 293.15

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2017
RadiationMonochromator: a single-bounce silicon (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.2→45 Å / Num. obs: 3774695 / % possible obs: 99.87 % / Redundancy: 106.1 % / Biso Wilson estimate: 9.2 Å2 / CC1/2: 0.96 / CC star: 0.99 / Net I/σ(I): 50.08
Reflection shellResolution: 1.214→1.257 Å / Redundancy: 104.6 % / Num. unique obs: 3510 / CC1/2: 0.86 / CC star: 0.96 / % possible all: 99.24

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.21→45 Å / SU ML: 0.0952 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 15.9585
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.171 1788 5.03 %
Rwork0.1372 33731 -
obs0.1389 3774695 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15 Å2
Refinement stepCycle: LAST / Resolution: 1.21→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1121 0 40 159 1320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00521228
X-RAY DIFFRACTIONf_angle_d0.92691683
X-RAY DIFFRACTIONf_chiral_restr0.0789181
X-RAY DIFFRACTIONf_plane_restr0.0084216
X-RAY DIFFRACTIONf_dihedral_angle_d20.9115448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21-1.250.20141140.17262583X-RAY DIFFRACTION99.08
1.25-1.280.22371460.17132564X-RAY DIFFRACTION99.78
1.28-1.320.23191400.16062577X-RAY DIFFRACTION99.82
1.32-1.370.19041280.14812586X-RAY DIFFRACTION99.96
1.37-1.430.17871230.14292604X-RAY DIFFRACTION99.96
1.43-1.490.15251470.13012566X-RAY DIFFRACTION99.96
1.49-1.570.15831290.11762589X-RAY DIFFRACTION99.93
1.57-1.670.15711520.11452591X-RAY DIFFRACTION100
1.67-1.80.15211240.11982612X-RAY DIFFRACTION100
1.8-1.980.13981390.12482576X-RAY DIFFRACTION99.96
1.98-2.270.17161380.12842614X-RAY DIFFRACTION100
2.27-2.850.15251430.14862613X-RAY DIFFRACTION99.96
2.85-450.18481650.14022656X-RAY DIFFRACTION99.96

+
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