[English] 日本語
Yorodumi
- PDB-6r3w: M.tuberculosis nitrobindin with a water molecule coordinated to t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6r3w
TitleM.tuberculosis nitrobindin with a water molecule coordinated to the heme iron atom
ComponentsUPF0678 fatty acid-binding protein-like protein ERS007657_00996
KeywordsPROTEIN BINDING / heme-protein / beta-barrel / peroxynitrite detossification
Function / homology
Function and homology information


peroxynitrite isomerase activity / Isomerases; Other isomerases / heme binding / metal ion binding
Similarity search - Function
: / Nitrobindin, bacteria/plant / THAP4-like, heme-binding beta-barrel domain / Nitrobindin family / THAP4-like, heme-binding beta-barrel domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Peroxynitrite isomerase / Peroxynitrite isomerase 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsDe Simone, G. / di Masi, A. / Polticelli, F. / Pesce, A. / Nardini, M. / Bolognesi, M. / Ciaccio, C. / Coletta, M. / Turilli, E.S. / Fasano, M. ...De Simone, G. / di Masi, A. / Polticelli, F. / Pesce, A. / Nardini, M. / Bolognesi, M. / Ciaccio, C. / Coletta, M. / Turilli, E.S. / Fasano, M. / Tognaccini, L. / Smulevich, G. / Abbruzzetti, S. / Viappiani, C. / Bruno, S. / Ascenzi, P.
CitationJournal: Antioxid.Redox Signal. / Year: 2020
Title: Mycobacterial and Human Nitrobindins: Structure and Function.
Authors: De Simone, G. / di Masi, A. / Vita, G.M. / Polticelli, F. / Pesce, A. / Nardini, M. / Bolognesi, M. / Ciaccio, C. / Coletta, M. / Turilli, E.S. / Fasano, M. / Tognaccini, L. / Smulevich, G. ...Authors: De Simone, G. / di Masi, A. / Vita, G.M. / Polticelli, F. / Pesce, A. / Nardini, M. / Bolognesi, M. / Ciaccio, C. / Coletta, M. / Turilli, E.S. / Fasano, M. / Tognaccini, L. / Smulevich, G. / Abbruzzetti, S. / Viappiani, C. / Bruno, S. / Ascenzi, P.
History
DepositionMar 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UPF0678 fatty acid-binding protein-like protein ERS007657_00996
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5572
Polymers18,9401
Non-polymers6161
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-18 kcal/mol
Surface area8260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.782, 74.295, 80.339
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-376-

HOH

-
Components

#1: Protein UPF0678 fatty acid-binding protein-like protein ERS007657_00996


Mass: 18940.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: ERS007657_00996, ERS007661_00585, ERS007665_01763, ERS007670_02052, ERS007672_00691, ERS007679_01339, ERS007681_01416, ERS007688_01403, ERS007703_01571, ERS007720_01340, ERS007722_02241, ...Gene: ERS007657_00996, ERS007661_00585, ERS007665_01763, ERS007670_02052, ERS007672_00691, ERS007679_01339, ERS007681_01416, ERS007688_01403, ERS007703_01571, ERS007720_01340, ERS007722_02241, ERS007726_02281, ERS007734_00360, ERS007737_00208, ERS007741_02326, ERS023446_01189, ERS024213_01977, ERS027644_00434, ERS027646_00714, ERS027651_02146, ERS027652_02045, ERS027653_02567, ERS027656_02331, ERS027659_01673, ERS027661_03351, ERS027666_00865, ERS031537_00196, ERS124361_02201, SAMEA2682864_02059, SAMEA2683035_01682
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
Strain (production host): BL21 / References: UniProt: A0A0E8TXJ8, UniProt: P9WFG7*PLUS
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.63 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.2 M MgCl2, 0.1 M Tris, PEG 4k 30%

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Jun 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.2→48.5 Å / Num. obs: 54078 / % possible obs: 95 % / Redundancy: 12.4 % / Net I/σ(I): 8.7
Reflection shellResolution: 1.2→1.26 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 6047 / % possible all: 74.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2fr2

2fr2


Resolution: 1.2→47.09 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.353 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.038 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17578 2685 5 %RANDOM
Rwork0.13978 ---
obs0.14157 51392 94.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.814 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0 Å20 Å2
2---0.04 Å2-0 Å2
3---0.14 Å2
Refinement stepCycle: 1 / Resolution: 1.2→47.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1224 0 43 219 1486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131349
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171242
X-RAY DIFFRACTIONr_angle_refined_deg1.3591.7071866
X-RAY DIFFRACTIONr_angle_other_deg0.9621.5982879
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.955174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.66321.23165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.62315208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5081510
X-RAY DIFFRACTIONr_chiral_restr0.0730.2173
X-RAY DIFFRACTIONr_gen_planes_refined0.0340.021547
X-RAY DIFFRACTIONr_gen_planes_other0.0270.02291
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7231.038659
X-RAY DIFFRACTIONr_mcbond_other1.4741.03658
X-RAY DIFFRACTIONr_mcangle_it2.0671.559826
X-RAY DIFFRACTIONr_mcangle_other2.1731.565827
X-RAY DIFFRACTIONr_scbond_it2.421.313690
X-RAY DIFFRACTIONr_scbond_other2.3891.308688
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.981.8691032
X-RAY DIFFRACTIONr_long_range_B_refined3.81514.4781464
X-RAY DIFFRACTIONr_long_range_B_other3.44413.371412
X-RAY DIFFRACTIONr_rigid_bond_restr4.82532590
X-RAY DIFFRACTIONr_sphericity_free24.9365162
X-RAY DIFFRACTIONr_sphericity_bonded10.32952614
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 136 -
Rwork0.228 2714 -
obs--68.87 %

+
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