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- PDB-8slb: X-ray structure of CorA N-terminal domain in complex with conform... -

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Basic information

Entry
Database: PDB / ID: 8slb
TitleX-ray structure of CorA N-terminal domain in complex with conformation-specific synthetic antibody C12
Components
  • Cobalt/magnesium transport protein CorA
  • sAB C12 Heavy Chain
  • sAB C12 Light Chain
KeywordsMETAL TRANSPORT / ion channel / magnesium channel / regulatory domain / divalent metal cation binding protein / MEMBRANE PROTEIN
Function / homology
Function and homology information


cobalt ion transport / magnesium ion transmembrane 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/cobalt transport protein CorA / Mg2+ transporter protein, CorA-like/Zinc transport protein ZntB / CorA, cytoplasmic domain / CorA, transmembrane region / CorA-like Mg2+ transporter protein / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cobalt/magnesium transport protein CorA
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsDominik, P.K. / Erramilli, S.K. / Reddy, B.G. / Kossiakoff, A.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117372 United States
Citation
Journal: J.Mol.Biol. / Year: 2023
Title: Conformation-specific Synthetic Antibodies Discriminate Multiple Functional States of the Ion Channel CorA.
Authors: Erramilli, S.K. / Dominik, P.K. / Deneka, D. / Tokarz, P. / Kim, S.S. / Reddy, B.G. / Skrobek, B.M. / Dalmas, O. / Perozo, E. / Kossiakoff, A.A.
#1: Journal: Biorxiv / Year: 2023
Title: Conformation-specific synthetic antibodies discriminate multiple functional states of the ion channel CorA.
Authors: Erramilli, S.K. / Dominik, P.K. / Deneka, D. / Tokarz, P. / Kim, S.S. / Reddy, B.G. / Skrobek, B.M. / Dalmas, O. / Perozo, E. / Kossiakoff, A.A.
History
DepositionApr 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Database references / Category: citation / citation_author
Revision 1.2Jul 26, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: Cobalt/magnesium transport protein CorA
H: sAB C12 Heavy Chain
L: sAB C12 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8056
Polymers83,6983
Non-polymers1063
Water10,539585
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-48 kcal/mol
Surface area31630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.338, 44.527, 150.634
Angle α, β, γ (deg.)90.00, 108.01, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Cobalt/magnesium transport protein CorA


Mass: 34277.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Gene: corA, TM_0561
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9WZ31
#2: Antibody sAB C12 Heavy Chain


Mass: 25984.107 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody sAB C12 Light Chain


Mass: 23437.037 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 585 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.7 Å3/Da / Density % sol: 54.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 8% dextrane sulfate, 17% PEG 3350, 0.02 M citric acid/0.08 M bis-Tris propane pH 8.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 15, 2015 / Details: 3.3 Undulator (Undulator A)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.038→45.82 Å / Num. obs: 55678 / % possible obs: 99.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.054 / Rrim(I) all: 0.078 / Net I/σ(I): 13.1
Reflection shellResolution: 2.04→2.09 Å / Rmerge(I) obs: 0.657 / Num. unique obs: 4041 / Rpim(I) all: 0.637 / Rrim(I) all: 0.918

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDS20190417data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→45.82 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.95 / SU B: 9.933 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21785 2747 4.9 %RANDOM
Rwork0.16559 ---
obs0.16826 52871 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.968 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å2-0 Å2-1.28 Å2
2---0.34 Å2-0 Å2
3---1.78 Å2
Refinement stepCycle: 1 / Resolution: 2.04→45.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5425 0 3 585 6013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0135603
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175115
X-RAY DIFFRACTIONr_angle_refined_deg1.8171.6487618
X-RAY DIFFRACTIONr_angle_other_deg1.3851.57211903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7025688
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52722.286280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95615942
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4941532
X-RAY DIFFRACTIONr_chiral_restr0.0870.2733
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026226
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021190
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0662.8692755
X-RAY DIFFRACTIONr_mcbond_other2.0662.8682754
X-RAY DIFFRACTIONr_mcangle_it3.0094.2843442
X-RAY DIFFRACTIONr_mcangle_other3.0094.2853443
X-RAY DIFFRACTIONr_scbond_it2.9223.2482848
X-RAY DIFFRACTIONr_scbond_other2.9233.2452846
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6164.7184176
X-RAY DIFFRACTIONr_long_range_B_refined7.23934.8676229
X-RAY DIFFRACTIONr_long_range_B_other7.10733.9686081
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.04→2.09 Å
RfactorNum. reflection% reflection
Rfree0.312 201 -
Rwork0.27 3837 -
obs--99.29 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7747-0.2694-0.26180.72040.35840.4152-0.00010.09520.1499-0.04720.0006-0.0563-0.016-0.0123-0.00050.1586-0.0031-0.08210.00550.00760.067-5.69535.2741-21.6136
22.18691.5483-1.358911.5159-0.34531.3538-0.0860.3406-0.0229-0.03570.2478-0.3692-0.1307-0.1721-0.16180.1379-0.0313-0.03950.0564-0.01150.21618.106627.1241-19.368
32.8220.72020.60983.50522.36631.8491-0.1462-0.1363-0.01330.04110.19-0.1244-0.01890.1274-0.04380.12910.0192-0.08650.025-0.01010.06576.22530.794-9.6154
49.44161.811110.06460.68133.567918.76620.30630.4806-0.23030.00090.025-0.06340.04220.1731-0.33140.03960.0078-0.01830.0698-0.00380.024721.54758.1715-3.1717
51.4995-0.32160.59340.2739-0.25820.69910.0083-0.02790.025-0.02330.03610.0380.0110.0174-0.04430.11160.0026-0.09610.011-0.00320.0891-36.82957.83-16.1336
61.50220.5423-0.24122.4916-2.15913.0869-0.3469-0.15290.41930.35180.1636-0.1491-0.2807-0.31940.18320.18910.0677-0.16270.064-0.07190.1601-68.3886-9.4499-17.4103
75.03566.6413-0.162216.3911-0.36091.4218-0.1728-0.43960.49680.37130.08970.79290.0643-0.31220.08310.05820.0488-0.00590.1728-0.04510.0713-79.3948-11.3734-17.8061
82.35241.1355-0.77261.4036-0.12171.09080.0539-0.2037-0.13110.003-0.03510.02940.03520.1053-0.01880.1398-0.0114-0.10060.02530.0220.0873-34.4704-9.0166-4.4398
91.0573-0.54771.58491.0194-0.24093.0184-0.00370.0292-0.00390.0579-0.03250.03680.01040.02720.03620.0785-0.0291-0.05520.01250.02120.047-62.5585-24.2568-19.6237
101.5551-0.34991.4891.4354-0.36563.5448-0.03910.0318-0.0501-0.0151-0.01790.03730.0493-0.09720.05710.052-0.0203-0.03550.01290.00490.0423-64.0669-25.4264-20.5028
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 184
2X-RAY DIFFRACTION2A185 - 219
3X-RAY DIFFRACTION3A220 - 258
4X-RAY DIFFRACTION4A259 - 266
5X-RAY DIFFRACTION5H4 - 136
6X-RAY DIFFRACTION6H137 - 226
7X-RAY DIFFRACTION7H227 - 232
8X-RAY DIFFRACTION8L1 - 107
9X-RAY DIFFRACTION9L108 - 161
10X-RAY DIFFRACTION10L162 - 214

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