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- PDB-6d91: Crystal structure of the Deinococcus radiodurans Nramp/MntH dival... -

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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 transmembrane transporter activity / cadmium ion transmembrane transporter activity / symporter activity / cellular response to iron ion / 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 (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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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 (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 / Water


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

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Experimental details

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Experiment

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

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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

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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

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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 )

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