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- PDB-7m1u: Crystal structure of an archaeal CNNM, MtCorB, R235L mutant with ... -

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Basic information

Entry
Database: PDB / ID: 7m1u
TitleCrystal structure of an archaeal CNNM, MtCorB, R235L mutant with C-terminal deletion
ComponentsHemolysin, contains CBS domains
KeywordsMEMBRANE PROTEIN / CorB / CNNM / DUF21 / magnesium transporter
Function / homology
Function and homology information


flavin adenine dinucleotide binding / 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
Hemolysin, contains CBS domains
Similarity search - Component
Biological speciesMethanoculleus thermophilus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsChen, Y.S. / Kozlov, G. / 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
DepositionMar 15, 2021Deposition site: RCSB / Processing site: RCSB
SupersessionJun 16, 2021ID: 7LJ8
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
B: Hemolysin, contains CBS domains


Theoretical massNumber of molelcules
Total (without water)73,1822
Polymers73,1822
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-47 kcal/mol
Surface area29940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.168, 124.024, 86.261
Angle α, β, γ (deg.)90.000, 92.813, 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, contains CBS domains /


Mass: 36591.164 Da / Num. of mol.: 2 / Mutation: R235L
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) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: A0A1G8XA46

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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: 5.08 Å3/Da / Density % sol: 75.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate, pH 5.5; 50 mM Li2SO4; 11% PEG4000; 10 mM MgSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.52154 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 14, 2021
RadiationMonochromator: KOHZU double crystal monochromator (DCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.52154 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 15203 / % possible obs: 91.7 % / Redundancy: 6 % / CC1/2: 0.965 / Net I/σ(I): 16.3
Reflection shellResolution: 3.8→3.94 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 152 / CC1/2: 0.51 / % possible all: 78.7

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Processing

Software
NameVersionClassification
HKL-2000v7.20data reduction
HKL-2000v7.20data scaling
PHENIX1.18.2_3874phasing
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LJ6, 7LJ7

7lj6
PDB Unreleased entry

7lj7
PDB Unreleased entry


Resolution: 3.8→46.27 Å / SU ML: 0.6517 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.632
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.285 741 4.9 %
Rwork0.2426 14372 -
obs0.2448 10821 53.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 95.9 Å2
Refinement stepCycle: LAST / Resolution: 3.8→46.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4289 0 0 0 4289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00234340
X-RAY DIFFRACTIONf_angle_d0.43825944
X-RAY DIFFRACTIONf_chiral_restr0.0374795
X-RAY DIFFRACTIONf_plane_restr0.0027746
X-RAY DIFFRACTIONf_dihedral_angle_d14.2171424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-4.10.3275500.2683964X-RAY DIFFRACTION17.88
4.1-4.510.2824890.23721746X-RAY DIFFRACTION32.43
4.51-5.160.26021250.21322219X-RAY DIFFRACTION41.2
5.16-6.50.35272020.26784067X-RAY DIFFRACTION75.79
6.5-46.270.25762750.23925376X-RAY DIFFRACTION99.28
Refinement TLS params.Method: refined / Origin x: -12.7023134885 Å / Origin y: -30.0606052659 Å / Origin z: 23.9817900124 Å
111213212223313233
T0.633406380267 Å2-0.161621211985 Å2-0.0497215702869 Å2-0.880499039805 Å20.213168678047 Å2--0.626159223487 Å2
L0.720134707771 °2-0.534531863165 °20.0404677884708 °2-0.678996176286 °20.155788694607 °2--0.122841075342 °2
S0.0114315532564 Å °-0.15799547717 Å °-0.184172816174 Å °-0.181697482535 Å °0.0486718623698 Å °0.249748335253 Å °0.157468704409 Å °0.0645026804083 Å °-0.100869067574 Å °
Refinement TLS groupSelection details: all

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