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- PDB-2iub: Crystal structure of a divalent metal ion transporter CorA at 2.9... -

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Basic information

Entry
Database: PDB / ID: 2iub
TitleCrystal structure of a divalent metal ion transporter CorA at 2.9 A resolution.
ComponentsDIVALENT CATION TRANSPORT-RELATED PROTEIN
KeywordsMEMBRANE PROTEIN / CORA / DIVALENT CATION / ION TRANSPORTER
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 / OTHER / Resolution: 2.9 Å
AuthorsEshaghi, S. / Niegowski, D. / Kohl, A. / Martinez Molina, D. / Lesley, S.A. / Nordlund, P.
CitationJournal: Science / Year: 2006
Title: Crystal Structure of a Divalent Metal Ion Transporter Cora at 2.9 Angstrom Resolution.
Authors: Eshaghi, S. / Niegowski, D. / Kohl, A. / Martinez Molina, D. / Lesley, S.A. / Nordlund, P.
History
DepositionJun 1, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIVALENT CATION TRANSPORT-RELATED PROTEIN
B: DIVALENT CATION TRANSPORT-RELATED PROTEIN
C: DIVALENT CATION TRANSPORT-RELATED PROTEIN
D: DIVALENT CATION TRANSPORT-RELATED PROTEIN
E: DIVALENT CATION TRANSPORT-RELATED PROTEIN
F: DIVALENT CATION TRANSPORT-RELATED PROTEIN
G: DIVALENT CATION TRANSPORT-RELATED PROTEIN
H: DIVALENT CATION TRANSPORT-RELATED PROTEIN
I: DIVALENT CATION TRANSPORT-RELATED PROTEIN
J: DIVALENT CATION TRANSPORT-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)430,35638
Polymers429,59710
Non-polymers75928
Water23413
1
A: DIVALENT CATION TRANSPORT-RELATED PROTEIN
B: DIVALENT CATION TRANSPORT-RELATED PROTEIN
C: DIVALENT CATION TRANSPORT-RELATED PROTEIN
D: DIVALENT CATION TRANSPORT-RELATED PROTEIN
E: DIVALENT CATION TRANSPORT-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,20820
Polymers214,7995
Non-polymers40915
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27590 Å2
ΔGint-143.2 kcal/mol
Surface area82660 Å2
MethodPQS
2
F: DIVALENT CATION TRANSPORT-RELATED PROTEIN
G: DIVALENT CATION TRANSPORT-RELATED PROTEIN
H: DIVALENT CATION TRANSPORT-RELATED PROTEIN
I: DIVALENT CATION TRANSPORT-RELATED PROTEIN
J: DIVALENT CATION TRANSPORT-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,14818
Polymers214,7995
Non-polymers34913
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31940 Å2
ΔGint-194 kcal/mol
Surface area85520 Å2
MethodPQS
Unit cell
Length a, b, c (Å)116.230, 151.460, 143.320
Angle α, β, γ (deg.)90.00, 98.88, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
12A
22B
32C
42D
52E
62F
72G
82H
92I
102J
13A
23B
33C
43D
53E
63F
73G
83H
93I
103J

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALALYSLYSAA8 - 28620 - 298
21ALAALALYSLYSBB8 - 28620 - 298
31ALAALALYSLYSCC8 - 28620 - 298
41ALAALALYSLYSDD8 - 28620 - 298
51ALAALALYSLYSEE8 - 28620 - 298
61ALAALALYSLYSFF8 - 28620 - 298
71ALAALALYSLYSGG8 - 28620 - 298
81ALAALALYSLYSHH8 - 28620 - 298
91ALAALALYSLYSII8 - 28620 - 298
101ALAALALYSLYSJJ8 - 28620 - 298
12THRTHRTYRTYRAA287 - 311299 - 323
22THRTHRTYRTYRBB287 - 311299 - 323
32THRTHRTYRTYRCC287 - 311299 - 323
42THRTHRTYRTYRDD287 - 311299 - 323
52THRTHRTYRTYREE287 - 311299 - 323
62THRTHRTYRTYRFF287 - 311299 - 323
72THRTHRTYRTYRGG287 - 311299 - 323
82THRTHRTYRTYRHH287 - 311299 - 323
92THRTHRTYRTYRII287 - 311299 - 323
102THRTHRTYRTYRJJ287 - 311299 - 323
13TYRTYRLYSLYSAA327 - 349339 - 361
23TYRTYRLYSLYSBB327 - 349339 - 361
33TYRTYRLYSLYSCC327 - 349339 - 361
43TYRTYRLYSLYSDD327 - 349339 - 361
53TYRTYRLYSLYSEE327 - 349339 - 361
63TYRTYRLYSLYSFF327 - 349339 - 361
73TYRTYRLYSLYSGG327 - 349339 - 361
83TYRTYRLYSLYSHH327 - 349339 - 361
93TYRTYRLYSLYSII327 - 349339 - 361
103TYRTYRLYSLYSJJ327 - 349339 - 361

NCS ensembles :
ID
1
2
3

NCS oper: (Code: given
Matrix: (0.9574, 0.2784, -0.07667), (-0.02003, 0.3289, 0.9442), (0.2881, -0.9024, 0.3204)
Vector: 0.718, -3.592, -0.0532)

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Components

#1: Protein
DIVALENT CATION TRANSPORT-RELATED PROTEIN / CORA


Mass: 42959.703 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9WZ31
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.2 % / Description: NONE
Crystal growDetails: 0.1 M MGCL2 0.1 M NACL 10% PEG 1500 1.6 % OCTYL.GLUCOPYRANOSIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 97952 / % possible obs: 90.2 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.14

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.875 / SU B: 22.342 / SU ML: 0.416 / Cross valid method: THROUGHOUT / ESU R Free: 0.484 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. LOOP REGIONS SUBSTITUTET WITH ALA
RfactorNum. reflection% reflectionSelection details
Rfree0.291 4921 5 %RANDOM
Rwork0.26 ---
obs0.262 92996 90.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.57 Å2
Baniso -1Baniso -2Baniso -3
1-2.32 Å20 Å21.74 Å2
2--0.45 Å20 Å2
3----2.23 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27539 0 28 13 27580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02228114
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.97638106
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.37953333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.30823.641305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.053155172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.44615205
X-RAY DIFFRACTIONr_chiral_restr0.1120.24452
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0220741
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.260.213346
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3240.219669
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3240.2599
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4690.278
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5030.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7241.517137
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.294227584
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.574312186
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8334.510522
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2324tight positional0.060.05
12B2324tight positional0.070.05
13C2324tight positional0.060.05
14D2324tight positional0.070.05
15E2324tight positional0.070.05
16F2324tight positional0.070.05
17G2324tight positional0.070.05
18H2324tight positional0.070.05
19I2324tight positional0.070.05
110J2324tight positional0.070.05
21A195tight positional0.040.05
22B195tight positional0.050.05
23C195tight positional0.050.05
24D195tight positional0.050.05
25E195tight positional0.050.05
26F195tight positional0.050.05
27G195tight positional0.050.05
28H195tight positional0.060.05
29I195tight positional0.050.05
210J195tight positional0.050.05
31A181tight positional0.040.05
32B181tight positional0.040.05
33C181tight positional0.060.05
34D181tight positional0.030.05
35E181tight positional0.040.05
36F181tight positional0.040.05
37G181tight positional0.040.05
38H181tight positional0.040.05
39I181tight positional0.040.05
310J181tight positional0.040.05
11A2324tight thermal0.110.5
12B2324tight thermal0.110.5
13C2324tight thermal0.110.5
14D2324tight thermal0.120.5
15E2324tight thermal0.120.5
16F2324tight thermal0.110.5
17G2324tight thermal0.120.5
18H2324tight thermal0.120.5
19I2324tight thermal0.130.5
110J2324tight thermal0.110.5
21A195tight thermal0.060.5
22B195tight thermal0.070.5
23C195tight thermal0.070.5
24D195tight thermal0.080.5
25E195tight thermal0.070.5
26F195tight thermal0.080.5
27G195tight thermal0.080.5
28H195tight thermal0.080.5
29I195tight thermal0.060.5
210J195tight thermal0.070.5
31A181tight thermal0.050.5
32B181tight thermal0.040.5
33C181tight thermal0.050.5
34D181tight thermal0.040.5
35E181tight thermal0.060.5
36F181tight thermal0.060.5
37G181tight thermal0.050.5
38H181tight thermal0.050.5
39I181tight thermal0.050.5
310J181tight thermal0.050.5
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.4 363
Rwork0.354 6665

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