[English] 日本語
Yorodumi
- PDB-6d91: Crystal structure of the Deinococcus radiodurans Nramp/MntH dival... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6d91
TitleCrystal structure of the Deinococcus radiodurans Nramp/MntH divalent transition metal transporter in the outward-open, apo conformation
ComponentsDivalent metal cation transporter MntH
KeywordsTRANSPORT PROTEIN / divalent transition metal transporter / LeuT-fold / manganese importer / proton-coupled secondary transporter
Function / homology
Function and homology information


manganese ion transport / cadmium ion transmembrane transporter activity / manganese ion transmembrane transporter activity / iron ion transmembrane transport / symporter activity / metal ion binding / plasma membrane
Similarity search - Function
NRAMP family / Natural resistance-associated macrophage protein-like
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Divalent metal cation transporter MntH
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 = ATCC 13939 = DSM 20539 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.356 Å
AuthorsBozzi, A.T. / Zimanyi, C.M. / Nicoludis, J.M. / Gaudet, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM120996-01A1 United States
CitationJournal: Elife / Year: 2019
Title: Structures in multiple conformations reveal distinct transition metal and proton pathways in an Nramp transporter.
Authors: Bozzi, A.T. / Zimanyi, C.M. / Nicoludis, J.M. / Lee, B.K. / Zhang, C.H. / Gaudet, R.
History
DepositionApr 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 25, 2024Group: Source and taxonomy / Structure summary / Category: entity_src_gen / pdbx_entry_details / Item: _entity_src_gen.pdbx_gene_src_scientific_name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Divalent metal cation transporter MntH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7517
Polymers44,6121
Non-polymers2,1396
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.919, 75.508, 53.151
Angle α, β, γ (deg.)90.00, 98.07, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-602-

HOH

-
Components

#1: Protein Divalent metal cation transporter MntH


Mass: 44611.875 Da / Num. of mol.: 1 / Mutation: G223W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: mntH, DR_1709 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q9RTP8
#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H40O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 6
Details: 50 mM succinic acid, 20 mM spermidine, 100 mM MES, 26% PEG400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.356→38.14 Å / Num. obs: 10998 / % possible obs: 63.94 % / Redundancy: 4.4 % / Biso Wilson estimate: 37.61 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.1847 / Rpim(I) all: 0.07994 / Rrim(I) all: 0.2026 / Net I/σ(I): 8.83
Reflection shellResolution: 2.36→2.44 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.3829 / Mean I/σ(I) obs: 1.45 / Num. unique obs: 256 / CC1/2: 0.683 / Rpim(I) all: 0.3478 / Rrim(I) all: 0.5194 / % possible all: 15.6

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3211: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BU5

6bu5
PDB Unreleased entry


Resolution: 2.356→38.136 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.54
RfactorNum. reflection% reflectionSelection details
Rfree0.2989 1061 10.01 %Random Selection of 5%
Rwork0.2438 ---
obs0.2492 10604 63.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.356→38.136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3012 0 86 17 3115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023160
X-RAY DIFFRACTIONf_angle_d0.5244291
X-RAY DIFFRACTIONf_dihedral_angle_d17.5491841
X-RAY DIFFRACTIONf_chiral_restr0.036517
X-RAY DIFFRACTIONf_plane_restr0.003526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3562-2.46340.4374330.3068299X-RAY DIFFRACTION16
2.4634-2.59320.2926530.2923472X-RAY DIFFRACTION26
2.5932-2.75570.3262910.2876822X-RAY DIFFRACTION44
2.7557-2.96830.31161320.2761187X-RAY DIFFRACTION64
2.9683-3.26690.32541670.27871500X-RAY DIFFRACTION80
3.2669-3.73930.29681870.23741682X-RAY DIFFRACTION90
3.7393-4.70970.27611930.22631742X-RAY DIFFRACTION93
4.7097-38.14070.29982050.23051839X-RAY DIFFRACTION96
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)
12.21760.73020.28340.21430.13070.8105-0.0773-0.11260.08340.15920.0417-0.0087-0.007-0.1614-0.02810.1888-0.00640.06510.30420.02080.171227.0285-10.409415.9548
24.2626-0.4158-3.35832.71591.9564.63130.3546-0.0577-0.13690.7461-0.1246-0.07210.00110.1798-0.30840.5219-0.09780.01130.47890.04810.304922.7405-19.82932.9339
32.49410.54131.45151.1509-0.02492.42810.0036-0.1198-0.1957-0.0064-0.05260.10220.0102-0.00210.08030.2324-0.01670.07960.2731-0.00160.099224.58-17.95469.3397
44.8241-1.92654.04343.6616-3.12598.0739-0.022-1.08330.72160.40530.25060.23680.2565-1.4287-0.46040.39860.084-0.03450.5825-0.01730.57960.5003-17.126515.1706
52.29161.5964-1.38242.1327-1.83151.57110.13280.1748-0.27260.21530.1214-0.01330.0165-0.0143-0.18180.16780.02580.07280.2976-0.06180.181823.575-16.328723.4546
64.33831.9735-2.04516.1531-0.63334.92520.43010.641-0.02010.36980.13821.12-0.1377-0.9766-0.19690.2157-0.00620.08490.6016-0.08650.342520.6727-6.648730.5976
73.1714-0.68961.19142.6602-0.89691.73670.49070.0513-0.428-0.5553-0.19790.2249-0.35540.0616-0.21340.2891-0.02610.04080.29640.06120.149732.5149-1.36967.7817
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 40 through 146 )
2X-RAY DIFFRACTION2chain 'A' and (resid 147 through 172 )
3X-RAY DIFFRACTION3chain 'A' and (resid 173 through 286 )
4X-RAY DIFFRACTION4chain 'A' and (resid 287 through 309 )
5X-RAY DIFFRACTION5chain 'A' and (resid 310 through 343 )
6X-RAY DIFFRACTION6chain 'A' and (resid 344 through 379 )
7X-RAY DIFFRACTION7chain 'A' and (resid 380 through 436 )

+
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