[English] 日本語
Yorodumi
- PDB-4zow: Crystal structure of E. coli multidrug transporter MdfA in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zow
TitleCrystal structure of E. coli multidrug transporter MdfA in complex with chloramphenicol
ComponentsMultidrug transporter MdfA
KeywordsTRANSPORT PROTEIN / MFS family / Multi-drug antiporter / MDFA / Cm
Function / homology
Function and homology information


potassium:proton antiporter activity / sodium:proton antiporter activity / xenobiotic detoxification by transmembrane export across the plasma membrane / regulation of cellular pH / response to antibiotic / plasma membrane
Similarity search - Function
Sugar transporter, conserved site / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
CHLORAMPHENICOL / Multidrug transporter MdfA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å
AuthorsZhang, X.C. / Heng, J. / Zhao, Y. / Wang, X.
CitationJournal: Cell Res. / Year: 2015
Title: Substrate-bound structure of the E. coli multidrug resistance transporter MdfA
Authors: Heng, J. / Zhao, Y. / Liu, M. / Liu, Y. / Fan, J. / Wang, X. / Zhao, Y. / Zhang, X.C.
History
DepositionMay 7, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Data collection
Revision 1.2Sep 16, 2015Group: Database references
Revision 1.3Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Multidrug transporter MdfA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7142
Polymers42,3911
Non-polymers3231
Water23413
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-11 kcal/mol
Surface area16440 Å2
Unit cell
Length a, b, c (Å)93.852, 63.449, 99.726
Angle α, β, γ (deg.)90.000, 106.090, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Multidrug transporter MdfA / Chloramphenicol resistance pump Cmr


Mass: 42390.543 Da / Num. of mol.: 1 / Fragment: UNP residues 10-400 / Mutation: Q122R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: mdfA, cmlA, cmr, b0842, JW0826
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0AEY8
#2: Chemical ChemComp-CLM / CHLORAMPHENICOL


Mass: 323.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12Cl2N2O5 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: sodium acetate, PEG 400, magnesium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 11.7 % / Number: 135599 / Rmerge(I) obs: 0.142 / Χ2: 1.03 / D res high: 3 Å / D res low: 50 Å / Num. obs: 11581 / % possible obs: 99.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
6.465010.0991.02912.3
5.136.4610.1191.03813.7
4.485.1310.1061.01412.3
4.074.4810.1341.01512.2
3.784.0710.1891.01112.9
3.563.7810.2741.06213.1
3.383.5610.4141.06212.8
3.233.3810.5791.05210.7
3.113.2310.6411.0099.3
33.1110.7380.9777.2
ReflectionResolution: 2.45→50 Å / Num. obs: 21233 / % possible obs: 99.6 % / Redundancy: 6.4 % / Biso Wilson estimate: 49.78 Å2 / Rmerge(I) obs: 0.116 / Χ2: 1.023 / Net I/av σ(I): 16.882 / Net I/σ(I): 6.7 / Num. measured all: 136611
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.45-2.544.80.99620570.99797.3
2.54-2.645.30.78821050.95898.8
2.64-2.766.20.65220871.05699.6
2.76-2.96.50.46221201.008100
2.9-3.097.10.31521131.002100
3.09-3.327.10.24221461.067100
3.32-3.666.80.16521071.032100
3.66-4.196.90.121451.022100
4.19-5.2870.06721611.058100
5.28-506.70.06621921.00299.8

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHENIXphenix.refine: 1.8_1069refinement
PDB_EXTRACT3.15data extraction
DENZOdata reduction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.45→45.088 Å / FOM work R set: 0.8037 / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2354 1051 4.95 %
Rwork0.204 20161 -
obs0.2055 21212 98.68 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.94 Å2 / Biso mean: 53.39 Å2 / Biso min: 27.46 Å2
Refinement stepCycle: final / Resolution: 2.45→45.088 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2958 0 20 13 2991
Biso mean--67.53 47.21 -
Num. residues----391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033052
X-RAY DIFFRACTIONf_angle_d0.8444154
X-RAY DIFFRACTIONf_chiral_restr0.06497
X-RAY DIFFRACTIONf_plane_restr0.003506
X-RAY DIFFRACTIONf_dihedral_angle_d13.6721054
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4274-2.53790.33171210.27692315243691
2.5379-2.67170.30271600.23742469262999
2.6717-2.8390.26511280.209925462674100
2.839-3.05820.24381240.19525192643100
3.0582-3.36580.26871100.202825922702100
3.3658-3.85270.2191270.195625372664100
3.8527-4.8530.19291310.19125832714100
4.853-45.09530.23651500.206226002750100

+
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