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- PDB-6gdv: Structure of CutA from Synechococcus elongatus PCC7942 complexed ... -

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Basic information

Entry
Database: PDB / ID: 6gdv
TitleStructure of CutA from Synechococcus elongatus PCC7942 complexed with Bis-Tris molecule
ComponentsPeriplasmic divalent cation tolerance protein
KeywordsMETAL BINDING PROTEIN / alleged copper binding protein / PII superfamily / thermostable protein / ferredoxin fold
Function / homology
Function and homology information


response to metal ion
Similarity search - Function
Divalent ion tolerance protein, CutA / CutA1 divalent ion tolerance protein / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Periplasmic divalent cation tolerance protein
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTremino, L. / Rubio, V.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2014-58229-P Spain
Other governmentPrometeoII/2014/029 Spain
CitationJournal: Febs J. / Year: 2020
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
DepositionApr 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.pdbx_Rpim_I_all
Revision 1.2Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jun 2, 2021Group: Data collection / Category: diffrn_radiation_wavelength / diffrn_source
Item: _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list
Revision 1.4Jan 17, 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2034
Polymers43,9933
Non-polymers2091
Water2,432135
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.590, 96.550, 48.900
Angle α, β, γ (deg.)90.00, 97.35, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113B6 - 52
2113C6 - 52
1213B55 - 85
2213C55 - 85
1314B88 - 113
2314C88 - 113

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.987572, -0.078138, 0.136371), (0.075324, -0.526231, -0.846999), (0.137945, 0.846744, -0.513805)-4.06188, 102.37992, 42.76053

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Components

#1: Protein Periplasmic divalent cation tolerance protein


Mass: 14664.476 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (strain PCC 7942) (bacteria)
Strain: PCC 7942 / Gene: Synpcc7942_2261 / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q31KX8
#2: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.25 Å3/Da / Density % sol: 45.36 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M Bis-Tris pH 5.5, 0.2 M Li2SO4, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→48.32 Å / Num. obs: 20245 / % possible obs: 94.2 % / Redundancy: 2.7 % / Rpim(I) all: 0.076 / Net I/σ(I): 5.6
Reflection shellResolution: 2→2.05 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1498 / Rpim(I) all: 0.235 / % possible all: 93.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NAQ

1naq


Resolution: 2→48.32 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.906 / SU B: 12.281 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.195 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25502 667 3.3 %RANDOM
Rwork0.19231 ---
obs0.19437 19551 93.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.672 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å2-0 Å21.4 Å2
2---0.19 Å2-0 Å2
3----1.04 Å2
Refinement stepCycle: 1 / Resolution: 2→48.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2475 0 14 135 2624
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022585
X-RAY DIFFRACTIONr_bond_other_d0.0020.022387
X-RAY DIFFRACTIONr_angle_refined_deg1.571.9643551
X-RAY DIFFRACTIONr_angle_other_deg0.9535548
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8185339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.1725.283106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12415427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1471513
X-RAY DIFFRACTIONr_chiral_restr0.0930.2440
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212857
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02480
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_it0.9282.071308
X-RAY DIFFRACTIONr_mcbond_other0.9262.071307
X-RAY DIFFRACTIONr_mcangle_it1.53.0931633
X-RAY DIFFRACTIONr_mcangle_other1.53.0931634
X-RAY DIFFRACTIONr_scbond_it1.3032.2981277
X-RAY DIFFRACTIONr_scbond_other1.3032.2981277
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0863.3791909
X-RAY DIFFRACTIONr_long_range_B_refined3.75225.0862778
X-RAY DIFFRACTIONr_long_range_B_other3.75125.0922779
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
371medium positional0.670.5
606loose positional0.665
446tight thermal2.430.5
371medium thermal1.492
606loose thermal2.9810
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 41 -
Rwork0.232 1452 -
obs--92.5 %
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)
10.27490.0362-0.14960.588-0.36310.78190.0128-0.07190.04980.0372-0.0328-0.0099-0.0885-0.03690.020.03580.00060.00280.0367-0.02040.013826.962847.472359.6829
20.42450.1126-0.15440.29330.13920.4276-0.00140.0805-0.0144-0.01050.0165-0.0182-0.0505-0.0672-0.01510.02120.01070.00360.0222-0.00190.005928.152741.806242.1409
30.2013-0.0696-0.08850.12920.16610.82630.0275-0.0214-0.0798-0.005-0.01580.0201-0.0041-0.0108-0.01170.0141-0.0039-0.00790.02140.00570.036627.273729.297755.7739
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 113
2X-RAY DIFFRACTION2B6 - 112
3X-RAY DIFFRACTION3C3 - 112

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