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- PDB-7cfg: Structure of the transmembrane domain of the bacterial CNNM/CorC ... -

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Basic information

Entry
Database: PDB / ID: 7cfg
TitleStructure of the transmembrane domain of the bacterial CNNM/CorC family Mg2+ transporter in complex with Mg2+
ComponentsHemolysin
KeywordsTRANSPORT PROTEIN / transporter
Function / homology
Function and homology information


flavin adenine dinucleotide binding / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
Transporter-associated domain / Transporter associated domain / Transporter associated domain / Ion transporter-like, CBS domain / Cyclin M transmembrane N-terminal domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / CBS domain superfamily ...Transporter-associated domain / Transporter associated domain / Transporter associated domain / Ion transporter-like, CBS domain / Cyclin M transmembrane N-terminal domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile.
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Hemolysin
Similarity search - Component
Biological speciesThermus parvatiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsHuang, Y. / Jin, F. / Hattori, M.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: Sci Adv / Year: 2021
Title: Structural basis for the Mg 2+ recognition and regulation of the CorC Mg 2+ transporter.
Authors: Huang, Y. / Jin, F. / Funato, Y. / Xu, Z. / Zhu, W. / Wang, J. / Sun, M. / Zhao, Y. / Yu, Y. / Miki, H. / Hattori, M.
History
DepositionJun 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4116
Polymers18,2511
Non-polymers1,1595
Water00
1
A: Hemolysin
hetero molecules

A: Hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,82112
Polymers36,5032
Non-polymers2,31910
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area3570 Å2
ΔGint-74 kcal/mol
Surface area15340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.570, 83.120, 98.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Space group name HallC22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z
#8: -x+1/2,-y+1/2,z

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Components

#1: Protein Hemolysin / CorC


Mass: 18251.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus parvatiensis (bacteria) / Gene: AV541_07030 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A109QFA5
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
Has ligand of interestY

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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: 3.24 Å3/Da / Density % sol: 62.05 %
Crystal growTemperature: 291 K / Method: lipidic cubic phase / pH: 4
Details: 10 mM ZnCl2, 100 mM sodium acetate (pH 4.0), 40% polyethylene glycol 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→47.33 Å / Num. obs: 3734 / % possible obs: 90.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 70.43 Å2 / CC1/2: 0.978 / Net I/σ(I): 5.6
Reflection shellResolution: 3.2→3.39 Å / Num. unique obs: 1109 / CC1/2: 0.68

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→47.33 Å / SU ML: 0.4261 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.8685
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2787 374 10.02 %
Rwork0.2266 3360 -
obs0.2322 3734 90.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.48 Å2
Refinement stepCycle: LAST / Resolution: 3.2→47.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1177 0 43 0 1220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811245
X-RAY DIFFRACTIONf_angle_d1.19381690
X-RAY DIFFRACTIONf_chiral_restr0.0498205
X-RAY DIFFRACTIONf_plane_restr0.0081204
X-RAY DIFFRACTIONf_dihedral_angle_d16.9281430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.660.33441230.26711109X-RAY DIFFRACTION92.08
3.66-4.610.28391230.22761108X-RAY DIFFRACTION90.25
4.61-47.330.24911280.20861143X-RAY DIFFRACTION88.63

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