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- PDB-9ybi: Structure of the CBS pair domain from zebrafish magnesium transpo... -

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Basic information

Entry
Database: PDB / ID: 9ybi
TitleStructure of the CBS pair domain from zebrafish magnesium transporter CNNM2
ComponentsMetal transporter
KeywordsTRANSPORT PROTEIN / magnesium transporter / Bateman fold / adenosyl-binding domain / protein-binding domain
Function / homology
Function and homology information


magnesium ion homeostasis / magnesium ion transmembrane transporter activity / brain development / plasma membrane
Similarity search - Function
Metal transporter CNNM4-like, immunoglobulin-like domain / Ancient conserved domain protein family / Cyclin M transmembrane N-terminal domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / Ion transporter-like, CBS domain / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile.
Similarity search - Domain/homology
BENZAMIDINE / Metal transporter
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKozlov, G. / Mahbub, L. / Jin, M. / Gehring, K.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: To Be Published
Title: Structure of the CBS pair domain from zebrafish magnesium transporter CNNM2
Authors: Kozlov, G. / Mahbub, L. / Jin, M. / Gehring, K.
History
DepositionSep 17, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,9334
Polymers35,6932
Non-polymers2402
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-24 kcal/mol
Surface area15430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.907, 147.942, 151.897
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Space group name HallI2b2c
Symmetry operation#1: x,y,z
#2: x,-y,-z+1/2
#3: -x+1/2,y,-z
#4: -x,-y+1/2,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1
#7: -x+1,y+1/2,-z+1/2
#8: -x+1/2,-y+1,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 370 through 378 or (resid 379...
d_2ens_1(chain "B" and (resid 370 through 472 or (resid 473...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLYGLYASNASNAA370 - 4961 - 127
d_12PHEPHESERSERAA503 - 522134 - 153
d_21GLYGLYASNASNBB370 - 4961 - 127
d_22PHEPHESERSERBB503 - 522134 - 153

NCS oper: (Code: givenMatrix: (-0.999992909896, 0.000631767156008, -0.00371228071456), (0.00370287241407, -0.0142930636015, -0.999890992593), (-0.000684758153069, -0.999897649364, 0.014290622909) ...NCS oper: (Code: given
Matrix: (-0.999992909896, 0.000631767156008, -0.00371228071456), (0.00370287241407, -0.0142930636015, -0.999890992593), (-0.000684758153069, -0.999897649364, 0.014290622909)
Vector: -21.7581769801, -37.5032723364, -37.3413616616)

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Components

#1: Protein Metal transporter


Mass: 17846.416 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: cnnm2a, im:7136247, si:ch211-67n3.4 / Production host: Escherichia coli (E. coli) / References: UniProt: A2ATX7
#2: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 6.84 Å3/Da / Density % sol: 82.02 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 1.1 M ammonium tartrate pH 6.5, 2% (w/v) benzamidine hydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 31, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3→46.904 Å / Num. obs: 18551 / % possible obs: 99.5 % / Redundancy: 20.5 % / Biso Wilson estimate: 87.03 Å2 / CC1/2: 0.956 / Net I/σ(I): 2.1
Reflection shellResolution: 3→3.05 Å / Num. unique obs: 1746 / CC1/2: 0.362

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→46.9 Å / SU ML: 0.4372 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.9906
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2526 912 4.92 %
Rwork0.2351 17639 -
obs0.236 18551 92.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.48 Å2
Refinement stepCycle: LAST / Resolution: 3→46.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2225 0 18 8 2251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212284
X-RAY DIFFRACTIONf_angle_d0.55143110
X-RAY DIFFRACTIONf_chiral_restr0.0407380
X-RAY DIFFRACTIONf_plane_restr0.0038397
X-RAY DIFFRACTIONf_dihedral_angle_d3.7516310
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.6436512857 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.160.38511130.35382398X-RAY DIFFRACTION89.87
3.16-3.360.2971230.28412603X-RAY DIFFRACTION95.85
3.36-3.610.25441520.26832557X-RAY DIFFRACTION96.78
3.62-3.980.26911460.2292629X-RAY DIFFRACTION97.75
3.98-4.550.23621370.20462559X-RAY DIFFRACTION94.93
4.55-5.740.20771240.222442X-RAY DIFFRACTION88.82
5.74-46.90.25081170.22462451X-RAY DIFFRACTION85.92

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