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

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Basic information

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


flavin adenine dinucleotide binding / ATP binding / metal ion binding / membrane
Similarity search - Function
Transporter-associated domain / Transporter associated domain / Transporter associated domain / Cyclin M transmembrane N-terminal domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / Ion transporter-like, CBS domain / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / Domain in cystathionine beta-synthase and other proteins. ...Transporter-associated domain / Transporter associated domain / Transporter associated domain / Cyclin M transmembrane N-terminal domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / Ion transporter-like, CBS domain / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile.
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Hemolysin
Similarity search - Component
Biological speciesThermus parvatiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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 1.2Nov 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9604
Polymers16,4051
Non-polymers5563
Water1629
1
A: Hemolysin
hetero molecules

A: Hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9218
Polymers32,8092
Non-polymers1,1126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_455-x-1/2,-y+1/2,z1
Buried area4410 Å2
ΔGint-54 kcal/mol
Surface area13310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.890, 87.300, 201.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x,y+1/2,z+1/2
#6: x,-y+1/2,-z+1/2
#7: -x,y+1/2,-z+1/2
#8: -x,-y+1/2,z+1/2
#9: x+1/2,y,z+1/2
#10: x+1/2,-y,-z+1/2
#11: -x+1/2,y,-z+1/2
#12: -x+1/2,-y,z+1/2
#13: x+1/2,y+1/2,z
#14: x+1/2,-y+1/2,-z
#15: -x+1/2,y+1/2,-z
#16: -x+1/2,-y+1/2,z

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Components

#1: Protein Hemolysin


Mass: 16404.643 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-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 4.16 Å3/Da / Density % sol: 66.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 0.1 M CaCl2, 0.1 M HEPES pH 7.5 and 5% PEG 8000

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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: Oct 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→43.65 Å / Num. obs: 10115 / % possible obs: 98.2 % / Redundancy: 9.5 % / Biso Wilson estimate: 66.48 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.2
Reflection shellResolution: 2.45→2.65 Å / Num. unique obs: 1293 / CC1/2: 0.515

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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: 7CFH

7cfh


Resolution: 2.45→43.65 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2591 1012 10 %
Rwork0.2453 --
obs0.2466 10115 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→43.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1054 0 35 7 1096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041109
X-RAY DIFFRACTIONf_angle_d0.9031522
X-RAY DIFFRACTIONf_dihedral_angle_d18.196169
X-RAY DIFFRACTIONf_chiral_restr0.049180
X-RAY DIFFRACTIONf_plane_restr0.003191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.580.32541440.28981293X-RAY DIFFRACTION99
2.58-2.740.3321410.29091285X-RAY DIFFRACTION99
2.74-2.950.30921450.29511301X-RAY DIFFRACTION99
2.95-3.250.31071430.26281286X-RAY DIFFRACTION98
3.25-3.720.29991430.2591282X-RAY DIFFRACTION97
3.72-4.680.24411450.22291303X-RAY DIFFRACTION98
4.69-43.650.22121510.23411353X-RAY DIFFRACTION96

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