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- PDB-4iy4: Structural and ligand binding properties of the Bateman domain of... -

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Basic information

Entry
Database: PDB / ID: 4iy4
TitleStructural and ligand binding properties of the Bateman domain of human magnesium transporters CNNM2 and CNNM4
ComponentsMetal transporter CNNM2
KeywordsMETAL TRANSPORT / CBS domain / Bateman domain / Magnesium transport / magnesium sensor / cytosol
Function / homology
Function and homology information


magnesium ion homeostasis / intracellular manganese ion homeostasis / magnesium ion transmembrane transporter activity / basolateral plasma membrane / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Ancient conserved domain protein family / Ion transporter-like, CBS domain / Cyclin M transmembrane N-terminal domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / CBS-domain / CBS-domain / CBS domain superfamily / CBS domain / CBS domain ...Ancient conserved domain protein family / Ion transporter-like, CBS domain / Cyclin M transmembrane N-terminal domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / CBS-domain / CBS-domain / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / RmlC-like jelly roll fold / Roll / Alpha Beta
Similarity search - Domain/homology
Metal transporter CNNM2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsCorral-Rodriguez, M.A. / Stuiver, M. / Encinar, J.A. / Spiwok, V. / Gomez-Garcia, I. / Oyenarte, I. / Ereno-Orbea, J. / Terashima, H. / Accardi, A. / Diercks, T. ...Corral-Rodriguez, M.A. / Stuiver, M. / Encinar, J.A. / Spiwok, V. / Gomez-Garcia, I. / Oyenarte, I. / Ereno-Orbea, J. / Terashima, H. / Accardi, A. / Diercks, T. / Muller, D. / Martinez-Cruz, L.A.
CitationJournal: To be Published
Title: Structural and ligand binding properties of the Bateman domain of human magnesium transporters CNNM2 and CNNM4
Authors: Corral-Rodriguez, M.A. / Stuiver, M. / Encinar, J.A. / Spiwok, V. / Gomez-Garcia, I. / Oyenarte, I. / Ereno-Orbea, J. / Terashima, H. / Accardi, A. / Diercks, T. / Muller, D. / Martinez-Cruz, L.A.
History
DepositionJan 28, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metal transporter CNNM2
C: Metal transporter CNNM2


Theoretical massNumber of molelcules
Total (without water)35,7532
Polymers35,7532
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-24 kcal/mol
Surface area15480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.346, 103.346, 99.899
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Metal transporter CNNM2 / Ancient conserved domain-containing protein 2 / Cyclin-M2


Mass: 17876.420 Da / Num. of mol.: 2 / Fragment: CBS domain, UNP residues 429-584 / Mutation: T568I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNNM2 / Plasmid: pET101D/TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9H8M5

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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: 3.73 Å3/Da / Density % sol: 67.03 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 4.6
Details: 2.8M AMMONIUM CHLORIDE, 4mM MANGANESE (II) CHLORIDE, 100mM SODIUM ACETATE , pH 4.6, VAPOR DIFFUSION, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 18, 2012
RadiationMonochromator: ID14-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.9→46.218 Å / Num. all: 12501 / Num. obs: 12501 / % possible obs: 99.93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 59.59 Å2
Reflection shellHighest resolution: 2.9 Å / % possible all: 99.93

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Processing

Software
NameVersionClassification
DNAdata collection
PHENIXmodel building
PHENIX1.7.3_928refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→46.218 Å / FOM work R set: 0.8066 / SU ML: 0.39 / σ(F): 1.36 / Phase error: 25.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2898 617 4.94 %
Rwork0.2323 11882 -
obs0.2349 12499 99.91 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.094 Å2 / ksol: 0.334 e/Å3
Displacement parametersBiso max: 156.53 Å2 / Biso mean: 61.18 Å2 / Biso min: 6.62 Å2
Baniso -1Baniso -2Baniso -3
1-3.0459 Å20 Å2-0 Å2
2--3.0459 Å2-0 Å2
3----6.0917 Å2
Refinement stepCycle: LAST / Resolution: 2.9→46.218 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2431 0 0 0 2431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042473
X-RAY DIFFRACTIONf_angle_d0.7223342
X-RAY DIFFRACTIONf_chiral_restr0.051390
X-RAY DIFFRACTIONf_plane_restr0.003431
X-RAY DIFFRACTIONf_dihedral_angle_d13.222932
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.9001-3.19190.35231560.319528983054
3.1919-3.65360.3351510.2729093060
3.6536-4.60250.28871610.212329533114
4.6025-46.22360.2431490.205131223271

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