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- PDB-5jrw: Crystal structure of Thermotoga maritima mutant D89R/D253R -

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Basic information

Entry
Database: PDB / ID: 5jrw
TitleCrystal structure of Thermotoga maritima mutant D89R/D253R
ComponentsCobalt/magnesium transport protein CorA
KeywordsTRANSPORT PROTEIN
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 / Resolution: 3.3 Å
AuthorsKowatz, T. / Maguire, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM099665-04 United States
CitationJournal: To Be Published
Title: Crystal structure of Thermotoga maritima mutant D89R/D253R
Authors: Kowatz, T. / Maguire, M.
History
DepositionMay 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Other
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Cobalt/magnesium transport protein CorA
B: Cobalt/magnesium transport protein CorA
C: Cobalt/magnesium transport protein CorA
D: Cobalt/magnesium transport protein CorA
E: Cobalt/magnesium transport protein CorA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,74611
Polymers220,6005
Non-polymers1466
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24780 Å2
ΔGint-177 kcal/mol
Surface area69180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.671, 134.808, 177.373
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15B
25C
16B
26D
17B
27E
18C
28D
19C
29E
110D
210E

NCS domain segments:

Component-ID: _ / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA17 - 34939 - 371
21LEULEUBB17 - 34939 - 371
12LEULEUAA17 - 34839 - 370
22LEULEUCC17 - 34839 - 370
13LEULEUAA17 - 34839 - 370
23LEULEUDD17 - 34839 - 370
14LEULEUAA17 - 34839 - 370
24LEULEUEE17 - 34839 - 370
15LEULEUBB17 - 34839 - 370
25LEULEUCC17 - 34839 - 370
16LEULEUBB17 - 34839 - 370
26LEULEUDD17 - 34839 - 370
17LEULEUBB17 - 34839 - 370
27LEULEUEE17 - 34839 - 370
18THRTHRCC16 - 34838 - 370
28THRTHRDD16 - 34838 - 370
19THRTHRCC16 - 34838 - 370
29THRTHREE16 - 34838 - 370
110LEULEUDD12 - 34934 - 371
210LEULEUEE12 - 34934 - 371

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

#1: Protein
Cobalt/magnesium transport protein CorA


Mass: 44119.957 Da / Num. of mol.: 5 / Mutation: D89R, D253R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: corA, TM_0561 / Plasmid: pET-15b modified / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3) / References: UniProt: Q9WZ31
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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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: 3.35 Å3/Da / Density % sol: 63.3 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.2 M MgCl2, 0.1 M MES pH 6.0, 25% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.3→49 Å / Num. obs: 51552 / % possible obs: 95.5 % / Redundancy: 4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.103 / Net I/σ(I): 8
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.409 / Mean I/σ(I) obs: 1 / % possible all: 90.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I0U

4i0u


Resolution: 3.3→49 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.895 / SU B: 56.502 / SU ML: 0.418 / Cross valid method: THROUGHOUT / ESU R Free: 0.54 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27413 1979 4.5 %RANDOM
Rwork0.23665 ---
obs0.23835 41660 95.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 147.145 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 3.3→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14018 0 6 2 14026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01914332
X-RAY DIFFRACTIONr_bond_other_d0.0030.0214059
X-RAY DIFFRACTIONr_angle_refined_deg1.1561.96919425
X-RAY DIFFRACTIONr_angle_other_deg0.857332288
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.81851671
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.65423.333690
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.333152652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.50615115
X-RAY DIFFRACTIONr_chiral_restr0.060.22224
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02115626
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023297
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_it7.59110.6846699
X-RAY DIFFRACTIONr_mcbond_other7.58810.6846698
X-RAY DIFFRACTIONr_mcangle_it11.40816.0358365
X-RAY DIFFRACTIONr_mcangle_other11.40816.0358366
X-RAY DIFFRACTIONr_scbond_it8.74611.5827633
X-RAY DIFFRACTIONr_scbond_other8.74511.5837634
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other13.70517.07811061
X-RAY DIFFRACTIONr_long_range_B_refined18.64859555
X-RAY DIFFRACTIONr_long_range_B_other18.64859556
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 / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A204870.14
12B204870.14
21A203440.14
22C203440.14
31A203020.15
32D203020.15
41A207970.13
42E207970.13
51B206170.13
52C206170.13
61B202600.15
62D202600.15
71B209270.13
72E209270.13
81C201680.15
82D201680.15
91C206730.13
92E206730.13
101D205730.14
102E205730.14
LS refinement shellResolution: 3.293→3.378 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 135 -
Rwork0.335 2566 -
obs--81.9 %
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)
14.9567-0.32130.26410.83130.12980.91360.0209-0.34780.0170.58730.0816-0.16720.05030.2241-0.10240.44810.0201-0.15030.0939-0.01690.112112.7435-6.9853-14.4387
21.6694-1.0937-0.59751.2950.53590.94570.09350.04120.0520.21150.078-0.17450.1364-0.0152-0.17150.27280.029-0.01950.0238-0.01610.18334.8161-23.4807-32.925
32.4194-1.0236-1.86570.8770.96452.87190.14880.14240.1564-0.00370.1158-0.07220.0141-0.1227-0.26460.26170.01660.03750.07970.02690.1229-3.9731-9.4562-53.9858
42.92761.2069-1.55232.823-0.951.56690.1474-0.46180.04550.379-0.1372-0.6087-0.34040.2255-0.01020.42750.0112-0.03960.0817-0.03790.24229.43317.9586-23.4538
51.13270.3438-0.50951.6765-0.4750.8292-0.2254-0.2233-0.0844-0.54220.0577-0.36410.20260.140.16770.48480.03090.20830.06340.00020.1609-0.944916.6772-47.7552
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 349
2X-RAY DIFFRACTION2B17 - 349
3X-RAY DIFFRACTION3C17 - 349
4X-RAY DIFFRACTION4D17 - 349
5X-RAY DIFFRACTION5E17 - 349

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