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- PDB-5m8a: Crystal structure of Eremococcus coleocola manganese transporter ... -

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Basic information

Entry
Database: PDB / ID: 5m8a
TitleCrystal structure of Eremococcus coleocola manganese transporter mutant E129A
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: 3.9 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 1.3Jan 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)56,5711
Polymers56,5711
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 area21180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.100, 80.800, 96.400
Angle α, β, γ (deg.)90.00, 107.40, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Divalent metal cation transporter MntH


Mass: 56570.516 Da / Num. of mol.: 1 / Mutation: E129A
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: 4.98 Å3/Da / Density % sol: 75.28 %
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: 3.9→50 Å / Num. obs: 10000 / % possible obs: 98.4 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rrim(I) all: 0.064 / Net I/σ(I): 13.4
Reflection shellResolution: 3.9→4 Å / Mean I/σ(I) obs: 1.84 / Num. unique all: 943 / CC1/2: 0.79 / Rrim(I) all: 1.224 / % possible all: 98.3

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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: 3.9→11.996 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.74
RfactorNum. reflection% reflection
Rfree0.2618 479 4.98 %
Rwork0.2106 --
obs0.2131 9617 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.9→11.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3776 0 0 0 3776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023849
X-RAY DIFFRACTIONf_angle_d0.495248
X-RAY DIFFRACTIONf_dihedral_angle_d16.2221356
X-RAY DIFFRACTIONf_chiral_restr0.036658
X-RAY DIFFRACTIONf_plane_restr0.004642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9-4.43910.30391580.26753014X-RAY DIFFRACTION98
4.4391-5.50150.31461620.23113054X-RAY DIFFRACTION99
5.5015-11.99570.22961590.18923070X-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)
10.7557-0.57170.10861.22780.3220.22750.03550.1757-0.3812-0.2150.04270.03791.15581.9548-01.8049-0.29680.05232.06730.01111.5056-9.8854-8.6326-18.3555
23.63350.06370.83040.86320.99163.4974-0.27160.13920.22570.16650.2174-0.1093-0.08090.6243-01.49410.00410.02131.3593-0.05621.4305-14.2861-12.6548-22.3797
30.93450.84740.23513.3412-0.07793.0942-0.64270.0205-0.42590.06980.3380.15370.84221.2236-01.46780.1815-0.13521.7055-0.06011.3824-14.8324-21.739-26.7374
41.245-0.97071.50531.126-1.71831.91080.17280.3423-0.1981-1.60680.0795-1.0041-0.6715-0.43701.618-0.087-0.0081.5827-0.03781.7907-31.7056-13.1127-27.1027
50.9378-0.79220.65350.0704-0.05490.2881-0.2106-0.50070.67250.0241-0.13910.43790.8578-0.9428-01.8185-0.32-0.01412.2122-0.28722.0297-39.563-20.0753-19.9029
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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