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- PDB-5m87: Crystal structure of Eremococcus coleocola manganese transporter -

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Basic information

Entry
Database: PDB / ID: 5m87
TitleCrystal structure of Eremococcus coleocola manganese transporter
ComponentsDivalent metal cation transporter MntH
KeywordsTRANSPORT PROTEIN
Function / homologyNRAMP family / Natural resistance-associated macrophage protein-like / cadmium ion transmembrane transporter activity / manganese ion transmembrane transporter activity / iron ion transmembrane transport / symporter activity / metal ion binding / plasma membrane / Divalent metal cation transporter MntH
Function and homology information
Biological speciesEremococcus coleocola ACS-139-V-Col8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.3 Å
AuthorsManatschal, C. / Ehrnstorfer, I.A. / Arnold, F.M. / Laederach, J. / Dutzler, R.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Nat Commun / Year: 2017
Title: Structural and mechanistic basis of proton-coupled metal ion transport in the SLC11/NRAMP family.
Authors: Ehrnstorfer, I.A. / Manatschal, C. / Arnold, F.M. / Laederach, J. / Dutzler, R.
History
DepositionOct 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)57,1112
Polymers56,6291
Non-polymers4831
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-3 kcal/mol
Surface area21300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.200, 81.650, 96.230
Angle α, β, γ (deg.)90.00, 107.57, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Divalent metal cation transporter MntH


Mass: 56628.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eremococcus coleocola ACS-139-V-Col8 (bacteria)
Gene: mntH, HMPREF9257_1603 / Production host: Escherichia coli (E. coli) / References: UniProt: E4KPW4
#2: Sugar ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM

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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: 5.01 Å3/Da / Density % sol: 75.46 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 50 mM Tris-HCl pH 8.6 22,8% PEG 400 (v/v)

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.0, 0.9794, 0.9796, 0.9173
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 22, 2016
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97941
30.97961
40.91731
ReflectionResolution: 3.3→50 Å / Num. obs: 16757 / % possible obs: 99.7 % / Redundancy: 13.6 % / CC1/2: 0.998 / Rrim(I) all: 0.051 / Net I/σ(I): 26.6
Reflection shellResolution: 3.3→3.4 Å / Mean I/σ(I) obs: 1.8 / Num. unique all: 1441 / CC1/2: 0.865 / Rrim(I) all: 1.646 / % possible all: 99.6

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Processing

Software
NameVersionClassification
XDSdata scaling
SHELXCDphasing
SHARPphasing
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 3.3→12 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.61
RfactorNum. reflection% reflection
Rfree0.2771 795 4.87 %
Rwork0.2322 --
obs0.2344 16334 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.3→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3780 0 33 0 3813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023887
X-RAY DIFFRACTIONf_angle_d0.5295298
X-RAY DIFFRACTIONf_dihedral_angle_d16.6051368
X-RAY DIFFRACTIONf_chiral_restr0.037668
X-RAY DIFFRACTIONf_plane_restr0.004643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.5020.46531140.40022573X-RAY DIFFRACTION99
3.502-3.76460.39021330.3362563X-RAY DIFFRACTION99
3.7646-4.12940.29551360.26542567X-RAY DIFFRACTION99
4.1294-4.69530.28631370.21782593X-RAY DIFFRACTION100
4.6953-5.8020.32051370.23782596X-RAY DIFFRACTION100
5.802-11.99990.21691380.19392647X-RAY DIFFRACTION100
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)
11.16840.3177-0.70861.49670.64430.6803-0.0383-0.0626-0.1016-0.18470.17880.37950.51781.85010.00081.4172-0.39620.0421.76730.0311.2077-9.809-8.6389-18.339
23.27660.57662.066-0.46370.21631.727-0.2786-0.6207-0.10440.1914-0.12970.2889-0.28070.2636-01.54350.20060.1230.9563-0.05161.1295-20.7199-16.1949-17.4513
30.8369-0.7404-0.09920.4555-0.0570.23180.1034-0.537-0.51211.2077-0.2647-0.94820.31551.784201.87390.492-0.18481.5403-0.06621.4477-3.5882-31.931-21.4707
42.9556-0.4076-0.23581.5033-0.42241.8644-0.0375-0.01310.4616-0.37690.2344-0.1053-0.59160.61101.118-0.29450.03561.3539-0.08991.2664-11.7488-9.0172-29.1873
52.3805-1.09521.61972.4994-0.23140.92810.128-0.6695-0.0180.78050.10590.1466-1.04821.7790.0020.86520.036-0.18081.327-0.04321.0941-8.5197-21.363-23.527
61.78520.2614-1.0460.5453-0.45250.5971-0.08640.2586-0.33250.80630.0489-0.98922.96881.784301.99170.6170.00921.37860.05851.5557-15.1466-35.6172-25.5196
70.4677-0.64811.53141.145-1.27371.5224-0.3826-0.238-0.0717-0.40210.3769-0.0335-0.99410.577101.2821-0.05780.01891.1034-0.12261.2317-25.327-13.907-18.7219
80.5696-0.87041.71761.1849-1.74852.3709-0.5340.404-0.1295-0.17980.5529-0.85040.01650.57910.00171.2190.1478-0.04631.2433-0.03481.4449-31.6487-12.9705-27.0838
92.8001-1.77891.01451.0139-0.62110.4170.328-0.98280.26030.04370.074-0.32490.9931-1.0725-01.4079-0.20810.21891.5031-0.13121.6895-39.5587-19.8473-19.903
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 67 )
2X-RAY DIFFRACTION2chain 'A' and (resid 68 through 140 )
3X-RAY DIFFRACTION3chain 'A' and (resid 141 through 164 )
4X-RAY DIFFRACTION4chain 'A' and (resid 165 through 316 )
5X-RAY DIFFRACTION5chain 'A' and (resid 317 through 364 )
6X-RAY DIFFRACTION6chain 'A' and (resid 365 through 394 )
7X-RAY DIFFRACTION7chain 'A' and (resid 395 through 438 )
8X-RAY DIFFRACTION8chain 'A' and (resid 439 through 473 )
9X-RAY DIFFRACTION9chain 'A' and (resid 474 through 506 )

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