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- PDB-7cfk: Structure of the CBS domain of the bacterial CNNM/CorC family Mg2... -

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Basic information

Entry
Database: PDB / ID: 7cfk
TitleStructure of the CBS domain of the bacterial CNNM/CorC family Mg2+ transporter in complex with the novel inhibitor IGN95a
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
Chem-FX6 / Hemolysin
Similarity search - Component
Biological speciesThermus parvatiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHuang, Y. / Jin, F. / Hattori, M.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: Iscience / Year: 2021
Title: Identification and mechanistic analysis of an inhibitor of the CorC Mg 2+ transporter.
Authors: Huang, Y. / Mu, K. / Teng, X. / Zhao, Y. / Funato, Y. / Miki, H. / Zhu, W. / Xu, Z. / Hattori, M.
History
DepositionJun 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemolysin
B: Hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3605
Polymers40,6582
Non-polymers7023
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-29 kcal/mol
Surface area15360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.015, 60.513, 82.256
Angle α, β, γ (deg.)90.000, 93.780, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Hemolysin


Mass: 20328.869 Da / Num. of mol.: 2 / Mutation: C282A, T336I
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-FX6 / (2S)-2-[(6-azanyl-9H-purin-8-yl)sulfanyl]butanoic acid


Mass: 253.281 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11N5O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
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: 2.78 Å3/Da / Density % sol: 55.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6 / Details: 0.1 M KCl, 0.1 M MES pH 6.0, 32% w/v PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97092 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97092 Å / Relative weight: 1
ReflectionResolution: 2.9→45.41 Å / Num. obs: 19225 / % possible obs: 99.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 82.23 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.28
Reflection shellResolution: 2.9→3.08 Å / Num. unique obs: 1164 / CC1/2: 0.524

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CFI

7cfi


Resolution: 2.9→45.41 Å / SU ML: 0.5221 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.2366
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2759 1931 10.04 %
Rwork0.2099 17294 -
obs0.2165 19225 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.39 Å2
Refinement stepCycle: LAST / Resolution: 2.9→45.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2445 0 45 14 2504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01032535
X-RAY DIFFRACTIONf_angle_d1.33053466
X-RAY DIFFRACTIONf_chiral_restr0.0659419
X-RAY DIFFRACTIONf_plane_restr0.0077441
X-RAY DIFFRACTIONf_dihedral_angle_d18.087363
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.970.43341350.36631164X-RAY DIFFRACTION94.61
2.98-3.060.3941310.3431264X-RAY DIFFRACTION99.57
3.06-3.150.36281360.31151223X-RAY DIFFRACTION99.78
3.15-3.250.35031470.27031237X-RAY DIFFRACTION99.71
3.25-3.360.29981320.2771248X-RAY DIFFRACTION99.86
3.36-3.50.32911560.26571241X-RAY DIFFRACTION99.86
3.5-3.660.29221380.22671250X-RAY DIFFRACTION99.93
3.66-3.850.2831220.19291231X-RAY DIFFRACTION99.93
3.85-4.090.3081450.19211237X-RAY DIFFRACTION99.64
4.09-4.410.25271400.17171247X-RAY DIFFRACTION100
4.41-4.850.23161400.17411253X-RAY DIFFRACTION100
4.85-5.550.231400.19281229X-RAY DIFFRACTION100
5.55-6.980.31481390.22881244X-RAY DIFFRACTION99.28
6.99-45.410.22311300.17131226X-RAY DIFFRACTION97.98

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