[English] 日本語
Yorodumi
- PDB-6zgr: Crystal structure of a MFS transporter with bound 1-hydroxynaphth... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zgr
TitleCrystal structure of a MFS transporter with bound 1-hydroxynaphthalene-2-carboxylic acid at 2.67 Angstroem resolution
ComponentsL-lactate transporter
KeywordsMEMBRANE PROTEIN / L-lactate transporter / monocarboxylate transporter / SLC16 family
Function / homologyMajor facilitator superfamily / Major Facilitator Superfamily / symporter activity / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / plasma membrane / 1-hydroxynaphthalene-2-carboxylic acid / L-lactate transporter
Function and homology information
Biological speciesSyntrophobacter fumaroxidans MPOB (syntrophic propionate-oxidizing bacterium DSM 10017)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.46 Å
AuthorsKalbermatter, D. / Bosshart, P. / Bonetti, S. / Fotiadis, D.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_184980 Switzerland
CitationJournal: Commun Chem / Year: 2021
Title: The making of a potent L-lactate transport inhibitor
Authors: Bosshart, P.D. / Kalbermatter, D. / Bonetti, S. / Fotiadis, D.
History
DepositionJun 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
A: L-lactate transporter
B: L-lactate transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,9764
Polymers89,5992
Non-polymers3762
Water362
1
A: L-lactate transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9882
Polymers44,8001
Non-polymers1881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L-lactate transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9882
Polymers44,8001
Non-polymers1881
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.553, 199.572, 62.468
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 11 through 160 or resid 167 through 191 or resid 218 through 407))
21(chain B and (resid 11 through 160 or resid 167 through 407))

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
11TRPTRPILEILE(chain A and (resid 11 through 160 or resid 167 through 191 or resid 218 through 407))AA11 - 16011 - 160
12TRPTRPPROPRO(chain A and (resid 11 through 160 or resid 167 through 191 or resid 218 through 407))AA167 - 191167 - 191
13ASPASPPROPRO(chain A and (resid 11 through 160 or resid 167 through 191 or resid 218 through 407))AA218 - 407218 - 407
21TRPTRPILEILE(chain B and (resid 11 through 160 or resid 167 through 407))BB11 - 16011 - 160
22TRPTRPPROPRO(chain B and (resid 11 through 160 or resid 167 through 407))BB167 - 407167 - 407

-
Components

#1: Protein L-lactate transporter / SfMCT


Mass: 44799.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Syntrophobacter fumaroxidans MPOB (syntrophic propionate-oxidizing bacterium DSM 10017)
Gene: Sfum_3364 / Plasmid: pZUDF21-rbs-3C-10His / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: A0LNN5
#2: Chemical ChemComp-1HN / 1-hydroxynaphthalene-2-carboxylic acid


Mass: 188.179 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.6 Å3/Da / Density % sol: 65.85 % / Mosaicity: 0.11 °
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: zinc bromide, HEPES, jeffamine ED-2003

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.46→47.14 Å / Num. obs: 47962 / % possible obs: 100 % / Redundancy: 47.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.022 / Rrim(I) all: 0.145 / Net I/σ(I): 22 / Num. measured all: 2295711 / Scaling rejects: 48405
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allRrim(I) all% possible allRmerge(I) obs
2.46-2.5949.368960.19639.476281.73599.9
7.78-47.1435.616820.9990.010.06299.60.061

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.77 Å47.14 Å
Translation3.77 Å47.14 Å

-
Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
PHASER2.8.2phasing
PHENIX1.14_3228refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G9X
Resolution: 2.46→14.983 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 37.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.255 1519 5 %
Rwork0.2209 28858 -
obs0.2226 30377 63.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 226.37 Å2 / Biso mean: 102.4572 Å2 / Biso min: 31.44 Å2
Refinement stepCycle: final / Resolution: 2.46→14.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5749 0 28 2 5779
Biso mean--80.37 73.17 -
Num. residues----763
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3162X-RAY DIFFRACTION7.72TORSIONAL
12B3162X-RAY DIFFRACTION7.72TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4605-2.53950.3542300.31155558514
2.5395-2.62980.3521370.296371575218
2.6298-2.73450.32500.280393898823
2.7345-2.85810.2695650.26921236130130
2.8581-3.00770.29081000.2661919201947
3.0077-3.19440.3021550.26632953310872
3.1944-3.43830.25591990.24323766396592
3.4383-3.77930.23672170.220641264343100
3.7793-4.31470.25722170.201941234340100
4.3147-5.39350.24662210.211941824403100
5.3935-14.98290.25482280.220243454573100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.12931.496-2.08365.67490.55974.5348-0.2101-0.6864-0.7553-0.2285-0.0221-1.43220.58851.0130.01910.3230.12050.08610.6019-0.00220.614133.690423.581490.4551
21.8843-1.8342-0.57245.20422.32573.72090.24320.21620.2893-1.327-0.49160.4295-0.9029-0.4360.23930.64040.1571-0.17790.3421-0.05110.411394.085130.667674.0602
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'B' and resid 11 through 407)B11 - 407
2X-RAY DIFFRACTION2(chain 'A' and resid 7 through 420)A7 - 420

+
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