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- PDB-6t76: PII-like protein CutA from Nostoc sp. PCC 7120 in apo form -

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Basic information

Entry
Database: PDB / ID: 6t76
TitlePII-like protein CutA from Nostoc sp. PCC 7120 in apo form
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 / Periplasmic divalent cation tolerance protein
Function and homology information
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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_poly / pdbx_database_status / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls_group / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_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_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 / _pdbx_validate_rmsd_angle.auth_asym_id_1 / _pdbx_validate_rmsd_angle.auth_asym_id_2 / _pdbx_validate_rmsd_angle.auth_asym_id_3 / _pdbx_validate_rmsd_bond.auth_asym_id_1 / _pdbx_validate_rmsd_bond.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_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)80,11413
Polymers79,4416
Non-polymers6727
Water1,838102
1
A: Periplasmic divalent cation tolerance protein
B: Periplasmic divalent cation tolerance protein
D: Periplasmic divalent cation tolerance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0096
Polymers39,7213
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6990 Å2
ΔGint-88 kcal/mol
Surface area12320 Å2
MethodPISA
2
C: 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)40,1057
Polymers39,7213
Non-polymers3844
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-100 kcal/mol
Surface area12040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.133, 90.694, 93.707
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains A B
22Chains A C
33Chains A D
44Chains A E
55Chains A F
66Chains B C
77Chains B D
88Chains B E
99Chains B F
1010Chains C D
1111Chains C E
1212Chains C F
1313Chains D E
1414Chains D F
1515Chains E F

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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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)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: alr7093 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): LEMO21 / References: UniProt: Q8YL42
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 1.88 Å3/Da / Density % sol: 34.63 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bis-Tris pH 6.5, 2 M Ammonium sulphate.

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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: Dec 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→46.854 Å / Num. obs: 42415 / % possible obs: 99.7 % / Redundancy: 6.55 % / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Net I/av σ(I): 37.74 / Net I/σ(I): 13.4
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 6.34 % / Num. unique obs: 6637 / CC1/2: 0.749 / % possible all: 97.9

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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: 1V6H

1v6h


Resolution: 1.9→46.85 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / SU B: 11.116 / SU ML: 0.141 / Cross valid method: FREE R-VALUE / ESU R: 0.192 / ESU R Free: 0.154
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2258 2121 -
Rwork0.1985 --
all0.2 --
obs-42404 99.629 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.74 Å2
Baniso -1Baniso -2Baniso -3
1--1.226 Å2-0 Å20 Å2
2---0.653 Å20 Å2
3---1.879 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4901 0 35 102 5038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0195032
X-RAY DIFFRACTIONr_bond_other_d0.0110.024795
X-RAY DIFFRACTIONr_angle_refined_deg1.8011.9736844
X-RAY DIFFRACTIONr_angle_other_deg1.591311048
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7165612
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.07824.591220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79715876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1271524
X-RAY DIFFRACTIONr_chiral_restr0.1070.2803
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0215513
X-RAY DIFFRACTIONr_gen_planes_other0.0110.021056
X-RAY DIFFRACTIONr_nbd_refined0.230.2977
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.24715
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22437
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.22688
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.293
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.130.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.330.253
X-RAY DIFFRACTIONr_nbd_other0.3410.2134
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2370.29
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1150.22
X-RAY DIFFRACTIONr_mcbond_it1.7732.032466
X-RAY DIFFRACTIONr_mcbond_other1.7682.0292465
X-RAY DIFFRACTIONr_mcangle_it2.4893.0293072
X-RAY DIFFRACTIONr_mcangle_other2.4893.033073
X-RAY DIFFRACTIONr_scbond_it3.3652.5682566
X-RAY DIFFRACTIONr_scbond_other3.352.5652563
X-RAY DIFFRACTIONr_scangle_it5.0533.6873772
X-RAY DIFFRACTIONr_scangle_other5.0383.6843767
X-RAY DIFFRACTIONr_lrange_it6.63817.7975435
X-RAY DIFFRACTIONr_lrange_other6.62417.7275421
X-RAY DIFFRACTIONr_ncsr_local_group_10.10.056042
X-RAY DIFFRACTIONr_ncsr_local_group_20.0790.056126
X-RAY DIFFRACTIONr_ncsr_local_group_30.0720.056098
X-RAY DIFFRACTIONr_ncsr_local_group_40.0990.056126
X-RAY DIFFRACTIONr_ncsr_local_group_50.0780.055924
X-RAY DIFFRACTIONr_ncsr_local_group_60.0860.055987
X-RAY DIFFRACTIONr_ncsr_local_group_70.0910.055892
X-RAY DIFFRACTIONr_ncsr_local_group_80.0940.056069
X-RAY DIFFRACTIONr_ncsr_local_group_90.0750.055865
X-RAY DIFFRACTIONr_ncsr_local_group_100.0740.056086
X-RAY DIFFRACTIONr_ncsr_local_group_110.0770.056137
X-RAY DIFFRACTIONr_ncsr_local_group_120.0730.055924
X-RAY DIFFRACTIONr_ncsr_local_group_130.0830.055979
X-RAY DIFFRACTIONr_ncsr_local_group_140.0630.055953
X-RAY DIFFRACTIONr_ncsr_local_group_150.0820.055835
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
1.898-1.9470.3521480.3852811309995.48240.371
1.947-20.351510.3322858301299.90040.307
2-2.0580.341450.2942759290899.86240.264
2.058-2.1220.31440.2642732287799.96520.231
2.122-2.1910.2911390.232264027791000.203
2.191-2.2680.2471340.211255126851000.182
2.268-2.3530.2361290.203245925881000.172
2.353-2.4490.2361260.21239225181000.176
2.449-2.5580.2291200.1962273239499.95820.164
2.558-2.6820.2231160.183220523211000.156
2.682-2.8270.2651090.198207821871000.167
2.827-2.9970.2321040.199197420781000.173
2.997-3.2030.226980.191186419621000.167
3.203-3.4590.237920.187175318451000.168
3.459-3.7870.188850.1751608169499.9410.161
3.787-4.230.148770.158146015371000.15
4.23-4.8780.159690.129131213811000.132
4.878-5.9580.247590.195112011791000.188
5.958-8.3590.21470.22188793699.78630.215
8.359-46.8540.228290.22354857999.65460.248
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)
12.16830.33660.08791.94450.13711.81950.0386-0.2592-0.02150.3234-0.06060.14710.0057-0.00310.02210.06010.00820.02510.0761-0.00260.0938-6.68831.9171-5.8586
22.0667-0.75560.42352.27740.03131.9346-0.01060.0572-0.2967-0.0621-0.01940.26080.1698-0.10480.030.0219-0.01250.01680.0309-0.03590.1433-7.7756-4.1875-25.1854
32.5345-0.3504-0.14882.227-0.94521.46190.109-0.05370.22340.01530.0063-0.1067-0.32270.43-0.11530.0953-0.12840.03610.1776-0.0560.255321.3816.6365-23.2971
42.4868-0.0939-0.19543.2006-0.52350.42710.06250.04930.18990.0458-0.04860.0738-0.1436-0.0504-0.01390.05690.0192-0.00970.01950.0110.0863-8.062515.3713-20.9309
52.611-0.9390.5883.0901-0.20681.03990.08720.2529-0.1908-0.3016-0.0622-0.1160.10780.2101-0.0250.04390.02410.03750.1175-0.0450.165122.0894-3.4314-26.387
63.06330.37090.21161.96710.19392.39750.0357-0.3710.02630.4419-0.0374-0.1554-0.01210.13230.00170.10620.0148-0.03120.1486-0.01010.157923.02844.1616-7.9779
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 2021 - 200
22BB1 - 1041 - 200
33CC1 - 2001 - 200
44DD1 - 2001 - 200
55EE1 - 2001 - 201
66FF1 - 2001 - 200

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