[English] 日本語
Yorodumi
- PDB-3vvs: Crystal structure of MATE in complex with MaD3S -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vvs
TitleCrystal structure of MATE in complex with MaD3S
Components
  • Putative uncharacterized protein
  • macrocyclic peptide
KeywordsTRANSPORT PROTEIN/INHIBITOR / MATE / multidrug transporter / macrocyclic peptide / TRANSPORT PROTEIN / TRANSPORT PROTEIN-INHIBITOR complex
Function / homology: / Multi antimicrobial extrusion protein / MatE / antiporter activity / xenobiotic transmembrane transporter activity / plasma membrane / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / MATE family efflux transporter
Function and homology information
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTanaka, Y. / Ishitani, R. / Nureki, O.
CitationJournal: Nature / Year: 2013
Title: Structural basis for the drug extrusion mechanism by a MATE multidrug transporter.
Authors: Tanaka, Y. / Hipolito, C.J. / Maturana, A.D. / Ito, K. / Kuroda, T. / Higuchi, T. / Katoh, T. / Kato, H.E. / Hattori, M. / Kumazaki, K. / Tsukazaki, T. / Ishitani, R. / Suga, H. / Nureki, O.
History
DepositionJul 27, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Nov 8, 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 / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative uncharacterized protein
B: macrocyclic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,74414
Polymers50,4662
Non-polymers4,27812
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-21 kcal/mol
Surface area18150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.091, 59.970, 68.525
Angle α, β, γ (deg.)90.000, 91.840, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Putative uncharacterized protein / Archaeal-type transporter


Mass: 49276.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: JCM 8422 / Gene: PF0708 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q8U2X0
#2: Protein/peptide macrocyclic peptide / MaD3S


Mass: 1189.423 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Selected by the RaPID system protocol
#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C21H40O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 3.16 Å3/Da / Density % sol: 61.02 % / Mosaicity: 0.909 °
Crystal growTemperature: 293 K / Method: lipdic cubic phase / pH: 7
Details: 30% PEG 400, 100mM HEPES-NaOH, 100mM NaSCN, pH 7.0, lipdic cubic phase, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 0.979 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 27, 2011
RadiationMonochromator: liquid nitrogen cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 21796 / Num. obs: 21796 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.142 / Χ2: 1.161 / Net I/σ(I): 5.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.547.50.72711100.698199.9
2.54-2.597.60.63310890.7121100
2.59-2.647.60.63410760.7151100
2.64-2.697.60.5210850.7541100
2.69-2.757.60.42511080.7891100
2.75-2.827.60.41610690.8021100
2.82-2.897.60.39210920.8391100
2.89-2.967.70.3310970.8891100
2.96-3.057.60.28810750.9311100
3.05-3.157.60.248110411100
3.15-3.267.60.21910931.0141100
3.26-3.397.60.18810971.0931100
3.39-3.557.70.15210861.2841100
3.55-3.737.70.1311051.3911100
3.73-3.977.70.11311031.5491100
3.97-4.277.60.08510991.7781100
4.27-4.76.50.0859202.227184.8
4.7-5.387.60.08911261.9521100
5.38-6.787.60.08911121.5141100
6.78-507.30.0511501.565199.6

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VVN

3vvn


Resolution: 2.6→43.076 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.8309 / SU ML: 0.66 / σ(F): 1.36 / Phase error: 24.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2439 1792 9.25 %RANDOM
Rwork0.2129 ---
all0.2158 21796 --
obs0.2158 19376 99.05 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.399 Å2 / ksol: 0.309 e/Å3
Displacement parametersBiso max: 164.13 Å2 / Biso mean: 41.8136 Å2 / Biso min: 8.89 Å2
Baniso -1Baniso -2Baniso -3
1-8.5589 Å2-0 Å29.6856 Å2
2---3.9475 Å20 Å2
3----4.6115 Å2
Refinement stepCycle: LAST / Resolution: 2.6→43.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3354 0 181 40 3575
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023584
X-RAY DIFFRACTIONf_angle_d0.6484795
X-RAY DIFFRACTIONf_chiral_restr0.044575
X-RAY DIFFRACTIONf_plane_restr0.003567
X-RAY DIFFRACTIONf_dihedral_angle_d10.5131300
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6001-2.67030.25991430.21913261469100
2.6703-2.74890.27261320.206613591491100
2.7489-2.83760.26811410.212513391480100
2.8376-2.9390.26941410.203713631504100
2.939-3.05670.26641340.207813471481100
3.0567-3.19570.24371380.206813731511100
3.1957-3.36420.2541360.210513531489100
3.3642-3.57480.24461430.206213601503100
3.5748-3.85070.21231330.212313721505100
3.8507-4.23790.24481390.197113701509100
4.2379-4.85040.23461280.21351228135689
4.8504-6.10820.28831410.255813821523100
6.1082-43.08210.20661430.20951412155599
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.47040.10050.61611.8750.1871.45060.0207-0.01870.0186-0.0840.0447-0.0659-0.05150.1807-0.02910.09230.0387-0.0295-0.0033-0.00220.1022-36.909632.58296.3771
22.8668-0.8518-0.80631.28570.47331.27010.17450.110.074-0.1181-0.1427-0.3215-0.28420.2886-0.02460.1599-0.01790.00720.24040.02130.1321-22.203929.750714.2656
32.50820.33170.16661.40770.32730.609-0.1321-0.1444-0.1560.1220.1494-0.12130.20140.3705-0.05850.1350.0322-0.04830.23050.03120.1121-18.228621.336720.4578
43.8555-1.1338-1.45982.0836-1.46425.072-0.1894-0.2713-0.6274-0.2690.7818-0.13580.84380.9953-0.45941.1542-0.1114-0.02860.5237-0.16550.8603-27.788227.72895.7241
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 4:235)A4 - 235
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 236:309)A236 - 309
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 310:454)A310 - 454
4X-RAY DIFFRACTION4CHAIN BB0 - 10

+
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