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- PDB-4p1o: Crystal structure of the Bateman domain of murine magnesium trans... -

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Basic information

Entry
Database: PDB / ID: 4p1o
TitleCrystal structure of the Bateman domain of murine magnesium transporter CNNM2 bound to ATP-Mg
ComponentsMetal transporter CNNM2
KeywordsTRANSPORT PROTEIN / magnesium homeostasis / transport / hypomagnesemia / rare diseases / ACDP / Cyclin M
Function / homology
Function and homology information


magnesium ion transport / 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
ADENOSINE-5'-TRIPHOSPHATE / Metal transporter CNNM2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.06 Å
AuthorsCorral-Rodriguez, M.A. / Stuiver, M. / Abascal-Palacios, G. / Diercks, T. / Oyenarte, I. / Ereno-Orbea, J. / Encinar, J.A. / Spiwok, V. / Terashima, H. / Accardi, A. ...Corral-Rodriguez, M.A. / Stuiver, M. / Abascal-Palacios, G. / Diercks, T. / Oyenarte, I. / Ereno-Orbea, J. / Encinar, J.A. / Spiwok, V. / Terashima, H. / Accardi, A. / 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. / Abascal-Palacios, G. / Diercks, T. / Oyenarte, I. / Ereno-Orbea, J. / Encinar, J.A. / Spiwok, V. / Terashima, H. / Accardi, A. / Muller, D. / Martinez-Cruz, L.A.
History
DepositionFeb 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metal transporter CNNM2
B: Metal transporter CNNM2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8556
Polymers34,7922
Non-polymers1,0634
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-47 kcal/mol
Surface area15510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.633, 104.633, 99.861
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Metal transporter CNNM2 / Ancient conserved domain-containing protein 2 / mACDP2 / Cyclin-M2


Mass: 17395.861 Da / Num. of mol.: 2 / Fragment: UNP residues 430-580
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cnnm2, Acdp2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3TWN3
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*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: 3.93 Å3/Da / Density % sol: 68.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Sodium Acetate, 3.5M Ammonium Acetate, 5mM Magnesium chloride, 10mM ATP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 3.06→33.08 Å / Num. obs: 10982 / % possible obs: 96.04 % / Redundancy: 3.8 % / Biso Wilson estimate: 65.79 Å2 / Net I/σ(I): 12.43

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.06→33.08 Å / FOM work R set: 0.7956 / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2552 1061 10.09 %
Rwork0.2205 9453 -
obs0.224 10514 96.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 189.76 Å2 / Biso mean: 73.71 Å2 / Biso min: 38.54 Å2
Refinement stepCycle: final / Resolution: 3.06→33.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2434 0 64 0 2498
Biso mean--56.1 --
Num. residues----304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032548
X-RAY DIFFRACTIONf_angle_d0.8013452
X-RAY DIFFRACTIONf_chiral_restr0.051398
X-RAY DIFFRACTIONf_plane_restr0.003436
X-RAY DIFFRACTIONf_dihedral_angle_d14.494958
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.06-3.1990.341330.30291134126795
3.199-3.36750.27971290.25421181131097
3.3675-3.57820.28051280.26021156128496
3.5782-3.85410.23971190.22111176129597
3.8541-4.24130.25641370.1991174131196
4.2413-4.85340.21311330.19371174130796
4.8534-6.10840.23611420.21281203134596
6.1084-33.08980.26951400.21191255139594
Refinement TLS params.Method: refined / Origin x: 111.0417 Å / Origin y: 45.0052 Å / Origin z: -0.2612 Å
111213212223313233
T0.471 Å2-0.0403 Å2-0.0154 Å2-0.5003 Å2-0.0236 Å2--0.2851 Å2
L2.2522 °2-0.7384 °2-0.6384 °2-2.8511 °2-0.4199 °2--2.4923 °2
S-0.0027 Å °0.1552 Å °-0.1032 Å °0.0821 Å °-0.0249 Å °-0.065 Å °0.0308 Å °-0.0062 Å °0.0196 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA429 - 1000
2X-RAY DIFFRACTION1allB429 - 1000

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