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- PDB-4eeb: CorA coiled-coil mutant under Mg2+ absence -

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Basic information

Entry
Database: PDB / ID: 4eeb
TitleCorA coiled-coil mutant under Mg2+ absence
ComponentsMagnesium transport protein CorAMagnesium transporter
KeywordsMETAL TRANSPORT / trans-membrane protein / coiled-coil / Mg2+ channel / cesium binding / membrane
Function / homology
Function and homology information


magnesium ion transmembrane transport / cobalt ion transport / cobalt ion transmembrane transporter activity / magnesium ion transmembrane transporter activity / cobalt ion binding / protein homooligomerization / magnesium ion binding / identical protein binding / plasma membrane
Similarity search - Function
Magnesium transport protein CorA, transmembrane region / CorA soluble domain-like / Magnesium/cobalt transport protein CorA / CorA, cytoplasmic domain / CorA, transmembrane region / Mg2+ transporter protein, CorA-like/Zinc transport protein ZntB / CorA-like Mg2+ transporter protein / Beta Polymerase; domain 2 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle ...Magnesium transport protein CorA, transmembrane region / CorA soluble domain-like / Magnesium/cobalt transport protein CorA / CorA, cytoplasmic domain / CorA, transmembrane region / Mg2+ transporter protein, CorA-like/Zinc transport protein ZntB / CorA-like Mg2+ transporter protein / Beta Polymerase; domain 2 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Cobalt/magnesium transport protein CorA
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.8 Å
AuthorsPfoh, R. / Pai, E.F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural asymmetry in the magnesium channel CorA points to sequential allosteric regulation.
Authors: Pfoh, R. / Li, A. / Chakrabarti, N. / Payandeh, J. / Pomes, R. / Pai, E.F.
History
DepositionMar 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Magnesium transport protein CorA
B: Magnesium transport protein CorA
C: Magnesium transport protein CorA
D: Magnesium transport protein CorA
E: Magnesium transport protein CorA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,85415
Polymers194,6355
Non-polymers1,21910
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18560 Å2
ΔGint-115 kcal/mol
Surface area69100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.600, 221.900, 106.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 4 / Auth seq-ID: 26 - 349 / Label seq-ID: 5 - 328

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE

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Components

#1: Protein
Magnesium transport protein CorA / Magnesium transporter


Mass: 38927.016 Da / Num. of mol.: 5 / Mutation: R222A,K223A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: corA, TM_0561 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9WZ31
#2: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cs
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na

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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: 3.82 Å3/Da / Density % sol: 67.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Jeffamine M-600, CsCl, pH 6.5, temperature 277K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC CCD300 / Detector: CCD / Date: Jan 27, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3.8→19.92 Å / Num. all: 24030 / Num. obs: 24030 / % possible obs: 80.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 %
Reflection shellResolution: 3.8→3.9 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 760 / % possible all: 34.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MxDCdata collection
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IUB
Resolution: 3.8→19.92 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.868 / WRfactor Rfree: 0.3026 / WRfactor Rwork: 0.26 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.6428 / SU B: 263.88 / SU ML: 1.483 / SU Rfree: 1.0764 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3434 1189 4.9 %RANDOM
Rwork0.2987 ---
all0.3009 24030 --
obs0.3009 24030 80.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 339.55 Å2 / Biso mean: 159.6516 Å2 / Biso min: 108.56 Å2
Baniso -1Baniso -2Baniso -3
1-9.3 Å20 Å20 Å2
2---15.6 Å20 Å2
3---6.31 Å2
Refinement stepCycle: LAST / Resolution: 3.8→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12978 0 10 0 12988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02213244
X-RAY DIFFRACTIONr_bond_other_d0.0050.028992
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.9717961
X-RAY DIFFRACTIONr_angle_other_deg0.919321928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8351562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.57123.931636
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.101152417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2411590
X-RAY DIFFRACTIONr_chiral_restr0.0710.22102
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02114317
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022731
X-RAY DIFFRACTIONr_mcbond_it0.7451.57860
X-RAY DIFFRACTIONr_mcbond_other0.0741.53129
X-RAY DIFFRACTIONr_mcangle_it1.348212954
X-RAY DIFFRACTIONr_scbond_it0.79635384
X-RAY DIFFRACTIONr_scangle_it1.5074.55007
Refine LS restraints NCS

Ens-ID: 1 / Number: 4371 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.60.5
2BMEDIUM POSITIONAL0.690.5
3CMEDIUM POSITIONAL0.60.5
4DMEDIUM POSITIONAL0.590.5
5EMEDIUM POSITIONAL0.620.5
1AMEDIUM THERMAL0.222
2BMEDIUM THERMAL0.262
3CMEDIUM THERMAL0.252
4DMEDIUM THERMAL0.252
5EMEDIUM THERMAL0.192
LS refinement shellResolution: 3.8→3.895 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.456 28 -
Rwork0.414 682 -
all-710 -
obs-760 33.65 %
Refinement TLS params.Method: refined / Origin x: -30.707 Å / Origin y: -17.159 Å / Origin z: 28.003 Å
111213212223313233
T0.3362 Å2-0.0568 Å20.1091 Å2-2.5294 Å20.0103 Å2--0.6981 Å2
L1.6339 °2-0.5667 °20.8167 °2-0.5499 °20.3171 °2--1.478 °2
S0.1574 Å °0.0896 Å °-0.071 Å °-0.237 Å °0.0793 Å °-0.1838 Å °-0.2632 Å °0.1286 Å °-0.2367 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 349
2X-RAY DIFFRACTION1A401
3X-RAY DIFFRACTION1B26 - 349
4X-RAY DIFFRACTION1B1001 - 1004
5X-RAY DIFFRACTION1C26 - 349
6X-RAY DIFFRACTION1C401
7X-RAY DIFFRACTION1D26 - 349
8X-RAY DIFFRACTION1D1001
9X-RAY DIFFRACTION1E401
10X-RAY DIFFRACTION1E26 - 349
11X-RAY DIFFRACTION1E402 - 403

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