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- PDB-5m8k: Crystal structure of Eremococcus coleocola manganese transporter ... -

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Basic information

Entry
Database: PDB / ID: 5m8k
TitleCrystal structure of Eremococcus coleocola manganese transporter mutant E129Q
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 / MOLECULAR REPLACEMENT / Resolution: 3.6 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 29, 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 1.3Jan 17, 2024Group: 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

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Assembly

Deposited unit
A: Divalent metal cation transporter MntH


Theoretical massNumber of molelcules
Total (without water)56,6281
Polymers56,6281
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.260, 81.770, 96.500
Angle α, β, γ (deg.)90.00, 107.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Divalent metal cation transporter MntH


Mass: 56627.562 Da / Num. of mol.: 1 / Mutation: E129Q
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

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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: 5.02 Å3/Da / Density % sol: 75.51 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 50 mM Tris-HCl pH 8.6 22.6% PEG 400 (v/v)

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 13025 / % possible obs: 98.7 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rrim(I) all: 0.069 / Net I/σ(I): 12.8
Reflection shellResolution: 3.6→3.7 Å / Mean I/σ(I) obs: 1.78 / Num. unique all: 1033 / CC1/2: 0.817 / Rrim(I) all: 1.658 / % possible all: 99.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHENIX(1.11_2567: ???)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M87

5m87


Resolution: 3.6→11.997 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 35.92
RfactorNum. reflection% reflection
Rfree0.2652 632 5.01 %
Rwork0.2213 --
obs0.2234 12608 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.6→11.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3780 0 0 0 3780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023853
X-RAY DIFFRACTIONf_angle_d0.4945253
X-RAY DIFFRACTIONf_dihedral_angle_d16.1061359
X-RAY DIFFRACTIONf_chiral_restr0.036658
X-RAY DIFFRACTIONf_plane_restr0.003643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6001-3.86940.39551290.35322362X-RAY DIFFRACTION98
3.8694-4.24310.30311250.26922379X-RAY DIFFRACTION98
4.2431-4.82190.23521270.21332411X-RAY DIFFRACTION99
4.8219-5.94910.32031240.24692378X-RAY DIFFRACTION99
5.9491-11.99740.22981270.18982446X-RAY DIFFRACTION98
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)
11.4925-0.0464-0.53112.03610.54170.3629-0.39720.2855-0.2008-0.29290.28170.23720.94661.95901.6787-0.38060.05381.94410.09251.5892-10.0336-8.8517-18.4044
23.2661-0.77181.0981.53091.3433.835-0.26850.18840.27940.1960.1716-0.0898-0.38230.992601.3296-0.08030.00581.2442-0.03561.3249-14.4683-12.8698-22.4172
31.93220.51410.09523.5731-0.02813.5727-0.6230.0729-0.50570.050.33710.090.72481.1495-01.42910.1652-0.10891.6772-0.0721.5257-15.0673-21.9107-26.8044
40.3118-0.3270.81370.9332-1.28491.62130.13410.51780.0038-1.73420.0097-1.1875-0.733-0.110701.2770.0576-0.05251.3468-0.03991.597-31.9278-13.2798-26.9948
50.6692-0.2320.25440.5089-0.47860.4239-0.0713-0.82420.3413-0.43970.03220.54190.3485-0.647601.9652-0.22290.11872.2952-0.24292.2043-39.7365-20.261-19.7764
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 288 )
3X-RAY DIFFRACTION3chain 'A' and (resid 289 through 438 )
4X-RAY DIFFRACTION4chain 'A' and (resid 439 through 473 )
5X-RAY DIFFRACTION5chain 'A' and (resid 474 through 506 )

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