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

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Basic information

Entry
Database: PDB / ID: 7cfh
TitleStructure of the CBS domain of the bacterial CNNM/CorC family Mg2+ transporter
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
Biological speciesThermus parvatiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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 1.2Apr 3, 2024Group: 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

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Assembly

Deposited unit
A: Hemolysin
B: Hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1028
Polymers38,4032
Non-polymers6996
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-34 kcal/mol
Surface area16240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.520, 61.310, 81.830
Angle α, β, γ (deg.)90.00, 92.41, 90.00
Int Tables number5
Space group name H-MC121
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 / / CorC


Mass: 19201.701 Da / Num. of mol.: 2
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.77 Å3/Da / Density % sol: 55.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 4.5
Details: 0.4 M ammonium thiocyanate, 0.1 M sodium acetate pH 4.5, 15% PEG 4000

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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: Jan 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→44.5 Å / Num. obs: 30078 / % possible obs: 100 % / Redundancy: 8.6 % / Biso Wilson estimate: 39.91 Å2 / CC1/2: 0.995 / Net I/σ(I): 9.28
Reflection shellResolution: 2→2.12 Å / Num. unique obs: 1987 / CC1/2: 0.718

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology model

Resolution: 2→42.56 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2396 2005 6.67 %
Rwork0.2038 --
obs0.2062 30078 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→42.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2554 0 42 111 2707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092636
X-RAY DIFFRACTIONf_angle_d1.1773584
X-RAY DIFFRACTIONf_dihedral_angle_d7.979379
X-RAY DIFFRACTIONf_chiral_restr0.065424
X-RAY DIFFRACTIONf_plane_restr0.008458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.30151420.26511987X-RAY DIFFRACTION100
2.05-2.110.26491470.24781973X-RAY DIFFRACTION100
2.11-2.170.2821350.23912033X-RAY DIFFRACTION100
2.17-2.240.2751510.25311961X-RAY DIFFRACTION100
2.24-2.320.28421380.23521976X-RAY DIFFRACTION100
2.32-2.410.27521410.23142002X-RAY DIFFRACTION100
2.41-2.520.28951430.2221993X-RAY DIFFRACTION100
2.52-2.650.25141390.21572010X-RAY DIFFRACTION100
2.65-2.820.251470.22222014X-RAY DIFFRACTION100
2.82-3.040.23521410.22322010X-RAY DIFFRACTION100
3.04-3.340.28281400.21461998X-RAY DIFFRACTION100
3.34-3.820.22261440.20952025X-RAY DIFFRACTION100
3.83-4.820.21751450.16642019X-RAY DIFFRACTION100
4.82-42.560.20851520.18352072X-RAY DIFFRACTION100

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