[English] 日本語
Yorodumi
- PDB-6uw5: The crystal structure of FbiA from Mycobacterium smegmatis, GDP a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6uw5
TitleThe crystal structure of FbiA from Mycobacterium smegmatis, GDP and Fo bound form
ComponentsPhosphoenolpyruvate transferase
KeywordsBIOSYNTHETIC PROTEIN / Factor 420 / Phosphotransferase / Metalloenzyme
Function / homology
Function and homology information


2-phospho-L-lactate transferase / LPPG:FO 2-phospho-L-lactate transferase activity / magnesium ion binding
Similarity search - Function
CofD-like domain / Phosphoenolpyruvate transferase/2-phospho-L-lactate transferase / 2-phospho-L-lactate transferase CofD / CofD-like domain superfamily / 2-phospho-L-lactate transferase CofD / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-FO1 / GUANOSINE-5'-DIPHOSPHATE / Phosphoenolpyruvate transferase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGrinter, R. / Gillett, D. / Cordero, P.R.F. / Greening, C.
Funding support Australia, 3items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1178715 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1142699 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1139832 Australia
CitationJournal: mSystems / Year: 2020
Title: Cellular and Structural Basis of Synthesis of the Unique Intermediate Dehydro-F420-0 in Mycobacteria.
Authors: Grinter, R. / Ney, B. / Brammananth, R. / Barlow, C.K. / Cordero, P.R.F. / Gillett, D.L. / Izore, T. / Cryle, M.J. / Harold, L.K. / Cook, G.M. / Taiaroa, G. / Williamson, D.A. / Warden, A.C. ...Authors: Grinter, R. / Ney, B. / Brammananth, R. / Barlow, C.K. / Cordero, P.R.F. / Gillett, D.L. / Izore, T. / Cryle, M.J. / Harold, L.K. / Cook, G.M. / Taiaroa, G. / Williamson, D.A. / Warden, A.C. / Oakeshott, J.G. / Taylor, M.C. / Crellin, P.K. / Jackson, C.J. / Schittenhelm, R.B. / Coppel, R.L. / Greening, C.
History
DepositionNov 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Author supporting evidence / Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / pdbx_audit_support
Item: _audit_author.name / _citation.journal_id_ISSN
Revision 1.2Jun 3, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Phosphoenolpyruvate transferase
A: Phosphoenolpyruvate transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9919
Polymers69,5812
Non-polymers1,4107
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-54 kcal/mol
Surface area26800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.013, 73.647, 91.270
Angle α, β, γ (deg.)90.000, 95.230, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain B and (resid 1 through 93 or resid 100 through 326 or resid 401))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETSERSERchain AAB1 - 3261 - 326
21METMETVALVAL(chain B and (resid 1 through 93 or resid 100 through 326 or resid 401))BA1 - 931 - 93
22LEULEUSERSER(chain B and (resid 1 through 93 or resid 100 through 326 or resid 401))BA100 - 326100 - 326
23GDPGDPGDPGDP(chain B and (resid 1 through 93 or resid 100 through 326 or resid 401))BC401

-
Components

#1: Protein Phosphoenolpyruvate transferase / EPPG:FO PEP transferase


Mass: 34790.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: fbiA, MSMEG_1830, MSMEI_1787
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QTG2, 2-phospho-L-lactate transferase
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-FO1 / 1-deoxy-1-(8-hydroxy-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-D-ribitol / 7,8-didemethyl-8-hydroxy-5-deazariboflavin


Mass: 363.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17N3O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.21 Å3/Da / Density % sol: 44.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 18 % PEG6000, 0.1 M Tris, 0.2 M calcium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 29, 2019 / Details: Silicon
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.2→45.864 Å / Num. obs: 30975 / % possible obs: 100 % / Redundancy: 3.5 % / CC1/2: 0.971 / Rmerge(I) obs: 0.229 / Rpim(I) all: 0.168 / Net I/σ(I): 3.1
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 3.5 % / Rmerge(I) obs: 2.204 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2644 / CC1/2: 0.175 / Rpim(I) all: 1.623 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C3D

3c3d


Resolution: 2.2→45.821 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2626 1563 5.12 %
Rwork0.2059 28968 -
obs0.2088 30531 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.98 Å2 / Biso mean: 41.3258 Å2 / Biso min: 22.32 Å2
Refinement stepCycle: final / Resolution: 2.2→45.821 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4823 0 103 107 5033
Biso mean--53.43 35.43 -
Num. residues----646
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1968X-RAY DIFFRACTION12.201TORSIONAL
12B1968X-RAY DIFFRACTION12.201TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.2710.33631250.3014245993
2.271-2.35220.36571290.3042254095
2.3522-2.44640.38881370.2828260498
2.4464-2.55770.30371430.2679264599
2.5577-2.69250.31311380.25342642100
2.6925-2.86120.30151530.23752663100
2.8612-3.08210.29221540.22652672100
3.0821-3.39220.27581460.20342622100
3.3922-3.88280.2561530.17582686100
3.8828-4.8910.18121390.15082690100
4.891-45.8210.21371460.16672745100
Refinement TLS params.Method: refined / Origin x: 39.0302 Å / Origin y: 14.2258 Å / Origin z: 34.4565 Å
111213212223313233
T0.1711 Å2-0 Å2-0.0143 Å2-0.1753 Å2-0.0494 Å2--0.5393 Å2
L0.6145 °20.0078 °2-0.4994 °2-0.8188 °2-0.4478 °2--1.0451 °2
S0.0272 Å °0.127 Å °-0.096 Å °-0.0801 Å °-0.0077 Å °0.0992 Å °0.0328 Å °-0.0957 Å °-0.0127 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB1 - 326
2X-RAY DIFFRACTION1allB401 - 501
3X-RAY DIFFRACTION1allA1 - 326
4X-RAY DIFFRACTION1allA401
5X-RAY DIFFRACTION1allS2 - 128
6X-RAY DIFFRACTION1allC1 - 4

+
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