[English] 日本語
Yorodumi
- PDB-7esc: FmnB complexed with AMP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7esc
TitleFmnB complexed with AMP
ComponentsFAD:protein FMN transferase
KeywordsTRANSFERASE / Inhibitor / AMP / FMN transferase
Function / homology
Function and homology information


FAD:protein FMN transferase / transferase activity / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
Flavin transferase ApbE / ApbE family / ApbE-like superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / FAD:protein FMN transferase
Similarity search - Component
Biological speciesListeria monocytogenes serotype 1/2a
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.201 Å
AuthorsCheng, W. / Zheng, Y.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: MedComm (2020) / Year: 2022
Title: Structural insights into the catalytic and inhibitory mechanisms of the flavin transferase FmnB in Listeria monocytogenes.
Authors: Zheng, Y. / Yan, W. / Dou, C. / Zhou, D. / Chen, Y. / Jin, Y. / Yang, L. / Zeng, X. / Cheng, W.
History
DepositionMay 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FAD:protein FMN transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0853
Polymers37,7131
Non-polymers3722
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-13 kcal/mol
Surface area14540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.875, 67.872, 97.003
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein FAD:protein FMN transferase / Flavin transferase


Mass: 37713.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes serotype 1/2a (strain 10403S) (bacteria)
Gene: LMRG_02181
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0H3GJF7, FAD:protein FMN transferase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.13 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Potassium sodium tartrate tetrahydrate, 20% w/v Polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.2→39.46 Å / Num. obs: 16541 / % possible obs: 99 % / Redundancy: 2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.0447 / Net I/σ(I): 16.63
Reflection shellResolution: 2.2→2.279 Å / Num. unique obs: 1618 / CC1/2: 0.693

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5.8.0267refinement
xia20.7.7data reduction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ESA

7esa


Resolution: 2.201→39.46 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.919 / SU B: 24.866 / SU ML: 0.296 / Cross valid method: THROUGHOUT / ESU R: 0.398 / ESU R Free: 0.26
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.282 847 5.122 %
Rwork0.2447 15688 -
all0.247 --
obs-16535 99.453 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 51.749 Å2
Baniso -1Baniso -2Baniso -3
1--3.228 Å2-0 Å20 Å2
2--2.122 Å2-0 Å2
3---1.106 Å2
Refinement stepCycle: LAST / Resolution: 2.201→39.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2510 0 24 125 2659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132579
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172445
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.6443479
X-RAY DIFFRACTIONr_angle_other_deg1.4051.5955690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0465321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.94625.826115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.5415479
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.134154
X-RAY DIFFRACTIONr_chiral_restr0.0620.2343
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022884
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02519
X-RAY DIFFRACTIONr_nbd_refined0.1860.2557
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.22431
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21257
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21328
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.296
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.080.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1320.25
X-RAY DIFFRACTIONr_nbd_other0.1640.219
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2510.22
X-RAY DIFFRACTIONr_mcbond_it2.2133.491287
X-RAY DIFFRACTIONr_mcbond_other2.2133.4881286
X-RAY DIFFRACTIONr_mcangle_it3.3965.2281607
X-RAY DIFFRACTIONr_mcangle_other3.3955.231608
X-RAY DIFFRACTIONr_scbond_it2.8653.7551292
X-RAY DIFFRACTIONr_scbond_other2.8653.7551292
X-RAY DIFFRACTIONr_scangle_it4.4655.5351872
X-RAY DIFFRACTIONr_scangle_other4.4645.5341873
X-RAY DIFFRACTIONr_lrange_it7.33167.03310918
X-RAY DIFFRACTIONr_lrange_other7.31866.80910855
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.201-2.2580.555540.5761133X-RAY DIFFRACTION98.9992
2.258-2.320.445560.3891117X-RAY DIFFRACTION99.5755
2.32-2.3870.345440.3151084X-RAY DIFFRACTION99.1213
2.387-2.460.296480.2931046X-RAY DIFFRACTION99.0045
2.46-2.5410.415570.2841023X-RAY DIFFRACTION99.5392
2.541-2.630.308440.278999X-RAY DIFFRACTION99.3333
2.63-2.7290.317420.281957X-RAY DIFFRACTION99.6012
2.729-2.8410.265550.244923X-RAY DIFFRACTION99.1886
2.841-2.9670.343480.266886X-RAY DIFFRACTION99.893
2.967-3.1110.333630.245834X-RAY DIFFRACTION99.6667
3.111-3.280.289390.26812X-RAY DIFFRACTION99.6487
3.28-3.4780.348380.26780X-RAY DIFFRACTION99.3925
3.478-3.7180.3560.233705X-RAY DIFFRACTION99.8688
3.718-4.0160.237390.229690X-RAY DIFFRACTION99.7264
4.016-4.3980.287350.193624X-RAY DIFFRACTION99.6974
4.398-4.9160.229290.164584X-RAY DIFFRACTION99.8371
4.916-5.6740.188330.201500X-RAY DIFFRACTION99.8127
5.674-6.9430.252260.214444X-RAY DIFFRACTION100
6.943-9.7940.262290.167344X-RAY DIFFRACTION99.2021
Refinement TLS params.Method: refined / Origin x: 0.042 Å / Origin y: -1.2177 Å / Origin z: 16.639 Å
111213212223313233
T0.0454 Å2-0.0164 Å20.0175 Å2-0.2653 Å2-0.0399 Å2--0.0229 Å2
L1.4483 °20.7751 °20.1963 °2-2.2489 °2-0.4144 °2--1.4406 °2
S-0.1223 Å °-0.1039 Å °-0.0303 Å °-0.2127 Å °0.2618 Å °0.0031 Å °-0.1461 Å °-0.072 Å °-0.1395 Å °
Refinement TLS groupSelection: 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