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- PDB-7msu: Crystal structure of an archaeal CNNM, MtCorB, CBS-pair domain in... -

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Basic information

Entry
Database: PDB / ID: 7msu
TitleCrystal structure of an archaeal CNNM, MtCorB, CBS-pair domain in complex with Mg2+-ATP
ComponentsHemolysin, contains CBS domains
KeywordsMEMBRANE PROTEIN / CorB / CNNM / DUF21 / magnesium transporter / METAL TRANSPORT
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
ADENOSINE-5'-TRIPHOSPHATE / Hemolysin, contains CBS domains
Similarity search - Component
Biological speciesMethanoculleus thermophilus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsChen, Y.S. / Gehring, K.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2020-07195 Canada
CitationJournal: Nat Commun / Year: 2021
Title: Crystal structure of an archaeal CorB magnesium transporter.
Authors: Chen, Y.S. / Kozlov, G. / Moeller, B.E. / Rohaim, A. / Fakih, R. / Roux, B. / Burke, J.E. / Gehring, K.
History
DepositionMay 12, 2021Deposition site: RCSB / Processing site: RCSB
SupersessionJun 16, 2021ID: 7LJ6
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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

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Assembly

Deposited unit
A: Hemolysin, contains CBS domains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8305
Polymers15,2121
Non-polymers6184
Water1,00956
1
A: Hemolysin, contains CBS domains
hetero molecules

A: Hemolysin, contains CBS domains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,66010
Polymers30,4252
Non-polymers1,2368
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Unit cell
Length a, b, c (Å)52.100, 52.100, 112.284
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Space group name HallP4w2c
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+3/4
#8: -y,-x,-z+1/4
Components on special symmetry positions
IDModelComponents
11A-403-

MG

21A-529-

HOH

31A-553-

HOH

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Components

#1: Protein Hemolysin, contains CBS domains


Mass: 15212.321 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanoculleus thermophilus (archaea) / Gene: SAMN04488571_101329 / Plasmid: pET29a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0A1G8XA46
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MOPS, pH 7.0; 9% PEG 8000; 20 mM MgCl2, 5 mM ATP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2019
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 11974 / % possible obs: 99.8 % / Redundancy: 22 % / Biso Wilson estimate: 24.01 Å2 / CC1/2: 0.992 / Net I/σ(I): 38.4
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 12.4 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 294 / CC1/2: 0.721 / % possible all: 97.3

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Processing

Software
NameVersionClassification
HKL-2000v720data reduction
HKL-2000v720data scaling
PHENIX1.19.2_4158phasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YZ2

5yz2


Resolution: 2.07→38.19 Å / SU ML: 0.2655 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 29.2179
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2517 601 5.02 %
Rwork0.206 11369 -
obs0.2083 11970 66.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.9 Å2
Refinement stepCycle: LAST / Resolution: 2.07→38.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms930 0 37 56 1023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0017978
X-RAY DIFFRACTIONf_angle_d0.54191335
X-RAY DIFFRACTIONf_chiral_restr0.054164
X-RAY DIFFRACTIONf_plane_restr0.0034164
X-RAY DIFFRACTIONf_dihedral_angle_d12.021341
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.280.2763670.25311281X-RAY DIFFRACTION30.09
2.28-2.610.34641190.24812260X-RAY DIFFRACTION53.34
2.61-3.290.22291830.21483575X-RAY DIFFRACTION84.18
3.29-38.190.24392320.18984253X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: -12.4148336107 Å / Origin y: -9.85326114007 Å / Origin z: -3.16444258 Å
111213212223313233
T0.137857412517 Å20.0261138735591 Å20.0695205941717 Å2-0.399779513185 Å20.0301408973382 Å2--0.23487970648 Å2
L0.549112507789 °20.0576008462619 °2-0.120351226288 °2-0.281037031875 °20.252917614052 °2--0.44528882517 °2
S0.140530210982 Å °0.00990749859315 Å °0.173888610292 Å °-0.0798853692139 Å °0.0194215750072 Å °-0.124491983986 Å °-0.126667644096 Å °-0.042129524262 Å °0.00549688255522 Å °
Refinement TLS groupSelection details: all

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