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- PDB-4iy0: Structural and ligand binding properties of the Bateman domain of... -

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Basic information

Entry
Database: PDB / ID: 4iy0
TitleStructural and ligand binding properties of the Bateman domain of human magnesium transporters CNNM2 and CNNM4
ComponentsMetal transporter CNNM2
KeywordsMETAL TRANSPORT / CBS / Bateman domain / Magnesium Transporter / magnesium sensor / Cytosol
Function / homology
Function and homology information


magnesium ion homeostasis / magnesium ion transmembrane transporter activity / basolateral plasma membrane / ATP binding / plasma membrane
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
ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / Metal transporter CNNM2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metal transporter CNNM2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5286
Polymers17,8641
Non-polymers6635
Water2,090116
1
A: Metal transporter CNNM2
hetero molecules

A: Metal transporter CNNM2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,05512
Polymers35,7292
Non-polymers1,32710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_554-y+1/2,-x+1/2,-z-1/21
Buried area5260 Å2
ΔGint-47 kcal/mol
Surface area15230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.599, 104.599, 100.959
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-782-

HOH

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Components

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


Mass: 17864.365 Da / Num. of mol.: 1 / Fragment: CBS domain, UNP residues 429-584
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
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 3.86 Å3/Da / Density % sol: 68.17 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 4.6
Details: 10mM magnesium chloride, 3M ammonium acetate, 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: ID29 / Wavelength: 0.9793 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 4, 2012
RadiationMonochromator: ESRF ID29 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→73.96 Å / Num. all: 22264 / Num. obs: 22264 / % possible obs: 99.98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.6 % / Rsym value: 0.09
Reflection shellHighest resolution: 1.9 Å / % possible all: 99.98

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→42 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.609 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2296 1138 5.1 %RANDOM
Rwork0.20514 ---
obs0.20634 21125 99.97 %-
all-22264 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.805 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--0.3 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1215 0 31 116 1362
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0221272
X-RAY DIFFRACTIONr_angle_refined_deg2.4642.0071727
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4075153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.41925.66760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.49515231
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.914155
X-RAY DIFFRACTIONr_chiral_restr0.2620.2200
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021936
X-RAY DIFFRACTIONr_mcbond_it1.9781.5760
X-RAY DIFFRACTIONr_mcangle_it3.37121243
X-RAY DIFFRACTIONr_scbond_it4.513512
X-RAY DIFFRACTIONr_scangle_it7.1034.5483
LS refinement shellResolution: 1.903→1.952 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 90 -
Rwork0.303 1527 -
obs--99.88 %

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