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- PDB-6t7e: PII-like protein CutA from Nostoc sp. PCC7120 in complex with MES -

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Basic information

Entry
Database: PDB / ID: 6t7e
TitlePII-like protein CutA from Nostoc sp. PCC7120 in complex with MES
ComponentsPeriplasmic divalent cation tolerance protein
KeywordsSIGNALING PROTEIN / CutA / PII-like / cyanobacteria
Function / homologyDivalent ion tolerance protein, CutA / CutA1 divalent ion tolerance protein / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / response to metal ion / copper ion binding / Periplasmic divalent cation tolerance protein
Function and homology information
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsSelim, K.A. / Albrecht, R. / Forchhammer, K. / Hartmann, M.D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationFo195/9-2, RTG 1708-2 Germany
CitationJournal: Febs J. / Year: 2021
Title: Functional and structural characterization of PII-like protein CutA does not support involvement in heavy metal tolerance and hints at a small-molecule carrying/signaling role.
Authors: Selim, K.A. / Tremino, L. / Marco-Marin, C. / Alva, V. / Espinosa, J. / Contreras, A. / Hartmann, M.D. / Forchhammer, K. / Rubio, V.
History
DepositionOct 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 2.0Jun 2, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity_link / entity_poly / pdbx_database_status / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls_group / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / struct_conf / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site_anisotrop.pdbx_auth_asym_id ..._atom_site.auth_asym_id / _atom_site_anisotrop.pdbx_auth_asym_id / _entity_poly.pdbx_strand_id / _pdbx_database_status.pdb_format_compatible / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_refine_tls_group.beg_auth_asym_id / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _struct_conf.beg_auth_asym_id / _struct_conf.end_auth_asym_id / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq_dif.pdbx_pdb_strand_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.end_auth_asym_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site_gen.auth_asym_id
Revision 2.1Jan 24, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Periplasmic divalent cation tolerance protein
B: Periplasmic divalent cation tolerance protein
C: Periplasmic divalent cation tolerance protein
D: Periplasmic divalent cation tolerance protein
E: Periplasmic divalent cation tolerance protein
F: Periplasmic divalent cation tolerance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,22210
Polymers79,4416
Non-polymers7814
Water28816
1
A: Periplasmic divalent cation tolerance protein
C: Periplasmic divalent cation tolerance protein
hetero molecules

A: Periplasmic divalent cation tolerance protein
C: Periplasmic divalent cation tolerance protein
hetero molecules

A: Periplasmic divalent cation tolerance protein
C: Periplasmic divalent cation tolerance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,61312
Polymers79,4416
Non-polymers1,1716
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area18570 Å2
ΔGint-69 kcal/mol
Surface area20870 Å2
MethodPISA
2
B: Periplasmic divalent cation tolerance protein
D: Periplasmic divalent cation tolerance protein
hetero molecules

B: Periplasmic divalent cation tolerance protein
D: Periplasmic divalent cation tolerance protein
hetero molecules

B: Periplasmic divalent cation tolerance protein
D: Periplasmic divalent cation tolerance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0279
Polymers79,4416
Non-polymers5863
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area17040 Å2
ΔGint-90 kcal/mol
Surface area22370 Å2
MethodPISA
3
E: Periplasmic divalent cation tolerance protein
F: Periplasmic divalent cation tolerance protein
hetero molecules

E: Periplasmic divalent cation tolerance protein
F: Periplasmic divalent cation tolerance protein
hetero molecules

E: Periplasmic divalent cation tolerance protein
F: Periplasmic divalent cation tolerance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0279
Polymers79,4416
Non-polymers5863
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_435-y-1,x-y-2,z1
crystal symmetry operation3_645-x+y+1,-x-1,z1
Buried area16900 Å2
ΔGint-85 kcal/mol
Surface area22230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.073, 87.073, 152.994
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains A B C D E F)

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Components

#1: Protein
Periplasmic divalent cation tolerance protein


Mass: 13240.209 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Gene: alr7093 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): LEMO21 / References: UniProt: Q8YL42
#2: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.38 Å3/Da / Density % sol: 48.46 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 MES pH 6.5, 1.2 M Potassium/Sodium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→38.25 Å / Num. obs: 25325 / % possible obs: 99.8 % / Redundancy: 8.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Net I/σ(I): 16.98
Reflection shellResolution: 2.45→2.51 Å / Num. unique obs: 3985 / CC1/2: 0.842

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Processing

Software
NameVersionClassification
REFMAC5.8.0049 2013/06/30refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6T76

6t76


Resolution: 2.45→38.249 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.919 / SU B: 22.921 / SU ML: 0.238 / Cross valid method: FREE R-VALUE / ESU R: 0.592 / ESU R Free: 0.307
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2713 1267 -
Rwork0.2215 --
all0.224 --
obs-25325 99.783 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 60.286 Å2
Baniso -1Baniso -2Baniso -3
1-1.129 Å20.564 Å20 Å2
2--1.129 Å20 Å2
3----3.661 Å2
Refinement stepCycle: LAST / Resolution: 2.45→38.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4874 0 48 16 4938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195025
X-RAY DIFFRACTIONr_bond_other_d0.0010.024779
X-RAY DIFFRACTIONr_angle_refined_deg1.2431.9736834
X-RAY DIFFRACTIONr_angle_other_deg0.708311024
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0955609
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4424.646226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.96115858
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9321524
X-RAY DIFFRACTIONr_chiral_restr0.0650.2796
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215521
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021059
X-RAY DIFFRACTIONr_nbd_refined0.2020.2873
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1670.24397
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22367
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.22627
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.281
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0230.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2060.245
X-RAY DIFFRACTIONr_nbd_other0.1710.2275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1450.218
X-RAY DIFFRACTIONr_mcbond_it1.2183.1622454
X-RAY DIFFRACTIONr_mcbond_other1.2183.1622453
X-RAY DIFFRACTIONr_mcangle_it1.9454.7383057
X-RAY DIFFRACTIONr_mcangle_other1.9444.7383058
X-RAY DIFFRACTIONr_scbond_it1.6223.462569
X-RAY DIFFRACTIONr_scbond_other1.6223.462570
X-RAY DIFFRACTIONr_scangle_it2.5965.1043777
X-RAY DIFFRACTIONr_scangle_other2.5955.1043778
X-RAY DIFFRACTIONr_lrange_it4.0525.3415243
X-RAY DIFFRACTIONr_lrange_other4.0525.3445244
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
2.45-2.5140.305920.2941740185498.81340.261
2.514-2.5820.377890.2661687177799.94370.234
2.582-2.6570.276870.236165217391000.2
2.657-2.7380.269840.235160316871000.199
2.738-2.8280.311830.238157416571000.199
2.828-2.9260.318790.2641499158199.81020.214
2.926-3.0360.292770.23147315501000.191
3.036-3.1590.276740.221140514791000.186
3.159-3.2990.328720.233135914311000.204
3.299-3.4580.258690.235131013791000.211
3.458-3.6440.303650.2241239130699.84690.206
3.644-3.8620.266610.2011152122299.26350.187
3.862-4.1260.274580.207112111791000.194
4.126-4.4520.234550.188103910941000.183
4.452-4.8710.186510.173970102299.90220.176
4.871-5.4350.23460.19887291999.89120.2
5.435-6.2540.338420.25678883399.63990.241
6.254-7.6090.272350.2326717061000.226
7.609-10.5550.24290.1845505791000.205
10.555-38.2490.339190.32235437499.73260.334
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)
12.1016-0.525-0.50381.4191-0.17623.1722-0.03510.1106-0.288-0.0037-0.04620.04050.4562-0.13260.08120.0886-0.02860.00270.0154-0.01010.121741.8097-36.5923-32.5582
21.76890.2314-0.45830.88490.48022.30730.059-0.1072-0.05090.19170.018-0.3858-0.00760.2829-0.0770.0549-0.022-0.07610.058-0.02050.219355.2158-26.039-63.6135
32.62580.7025-0.12421.2129-0.42032.4825-0.0321-0.4169-0.37620.3065-0.05860.0380.50520.02890.09070.28290.00830.050.13240.06390.163441.7155-36.6292-3.3147
41.66830.332-0.02631.9093-0.2661.70730.13010.0439-0.0272-0.1902-0.1107-0.20140.09120.2311-0.01940.03840.02760.00980.0425-0.02080.144555.272-25.847-93.3254
54.3115-1.14660.79033.2155-0.16521.83270.05410.0850.46910.0374-0.0243-0.1741-0.20960.1095-0.02990.0542-0.04010.04980.0532-0.00310.364146.6867-64.2472-47.7992
60.14040.22340.19450.41070.48062.03440.1618-0.29550.06440.4247-0.33790.0329-0.46440.0510.17611.4342-0.0094-0.10761.224-0.26320.774647.3786-64.4757-18.418
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 2001 - 200
22BB1 - 2001 - 200
33CC1 - 2001 - 200
44DD1 - 1041 - 104
55EE1 - 2001 - 200
66FF3 - 1023 - 102

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