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- PDB-6dfd: Crystal structure of CNNM3 cyclic nucleotide-binding homology domain -

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Basic information

Entry
Database: PDB / ID: 6dfd
TitleCrystal structure of CNNM3 cyclic nucleotide-binding homology domain
ComponentsMetal transporter CNNM3
KeywordsMETAL TRANSPORT / beta-barrel fold / cyclic nucleotide-binding homology domain / magnesium transporter
Function / homology
Function and homology information


magnesium ion homeostasis / intracellular manganese ion homeostasis / transmembrane transporter activity / monoatomic ion transport / membrane / plasma membrane / cytoplasm
Similarity search - Function
Ancient conserved domain protein family / Ion transporter-like, CBS domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile.
Similarity search - Domain/homology
Metal transporter CNNM3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.901 Å
AuthorsKozlov, G. / Gehring, K.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: The cyclic nucleotide-binding homology domain of the integral membrane protein CNNM mediates dimerization and is required for Mg2+efflux activity.
Authors: Chen, Y.S. / Kozlov, G. / Fakih, R. / Funato, Y. / Miki, H. / Gehring, K.
History
DepositionMay 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metal transporter CNNM3
B: Metal transporter CNNM3


Theoretical massNumber of molelcules
Total (without water)58,8032
Polymers58,8032
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-5 kcal/mol
Surface area13810 Å2
Unit cell
Length a, b, c (Å)101.267, 101.267, 77.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Metal transporter CNNM3 / Ancient conserved domain-containing protein 3 / Cyclin-M3


Mass: 29401.285 Da / Num. of mol.: 2 / Mutation: I516M, T591M, A623M, L651M, V669M, I670M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNNM3, ACDP3 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8NE01
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 1.68 Å3/Da / Density % sol: 26.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.8 M succinic acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9773 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9773 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 32014 / % possible obs: 99.62 % / Redundancy: 28.7 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 44.2
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 27.5 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3117 / CC1/2: 0.662 / % possible all: 99.49

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.901→32.474 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.74
RfactorNum. reflection% reflection
Rfree0.2387 1587 4.96 %
Rwork0.2194 --
obs0.2205 32014 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.901→32.474 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2073 0 0 70 2143
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042112
X-RAY DIFFRACTIONf_angle_d0.6982862
X-RAY DIFFRACTIONf_dihedral_angle_d13.8461272
X-RAY DIFFRACTIONf_chiral_restr0.048336
X-RAY DIFFRACTIONf_plane_restr0.004360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9006-1.9620.35321270.31512721X-RAY DIFFRACTION99
1.962-2.03210.26741580.26492697X-RAY DIFFRACTION100
2.0321-2.11340.28261320.25282741X-RAY DIFFRACTION100
2.1134-2.20960.26891510.23232724X-RAY DIFFRACTION100
2.2096-2.32610.24761520.23622713X-RAY DIFFRACTION100
2.3261-2.47170.24821370.22582763X-RAY DIFFRACTION100
2.4717-2.66250.2581150.22712785X-RAY DIFFRACTION100
2.6625-2.93030.26261420.23132754X-RAY DIFFRACTION100
2.9303-3.35390.2191460.22412792X-RAY DIFFRACTION100
3.3539-4.22420.21961690.20612800X-RAY DIFFRACTION100
4.2242-32.4790.23631580.20682937X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 61.7563 Å / Origin y: 37.0256 Å / Origin z: 22.8207 Å
111213212223313233
T0.3711 Å2-0.0436 Å20.0047 Å2-0.2873 Å20.0207 Å2--0.3416 Å2
L2.4002 °2-0.8822 °21.148 °2-1.5222 °2-0.3913 °2--1.9759 °2
S0.232 Å °0.1267 Å °-0.0337 Å °-0.1823 Å °-0.1727 Å °-0.3004 Å °0.4041 Å °0.1697 Å °-0.0396 Å °
Refinement TLS groupSelection details: all

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