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- PDB-7b0e: Crystal structure of SmbA loop deletion mutant -

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Basic information

Entry
Database: PDB / ID: 7b0e
TitleCrystal structure of SmbA loop deletion mutant
ComponentsSmbA
KeywordsSIGNALING PROTEIN / c-di-GMP receptor / ppGpp receptor / second messenger / TIM barrel
Function / homologyNADP-dependent oxidoreductase domain superfamily / nucleotide binding / metal ion binding / Chem-C2E / NADP-dependent oxidoreductase domain-containing protein
Function and homology information
Biological speciesCaulobacter vibrioides CB15 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsDubey, B.N. / Schirmer, T.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_166652 Switzerland
CitationJournal: To Be Published
Title: High-resolution crystal structure of loop deletion mutant SmbA bound to a monomeric c-di-GMP
Authors: Dubey, B.N. / Shyp, V. / Jenal, U. / Schirmer, T.
History
DepositionNov 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 2.0Sep 7, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / chem_comp / entity / entity_src_gen / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] ..._atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_work / _software.classification / _software.name / _software.version
Description: Occupancy of atoms on special symmetry positions
Provider: author / Type: Coordinate replacement
Revision 2.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SmbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,64019
Polymers32,0391
Non-polymers1,60118
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
  • monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint17 kcal/mol
Surface area13950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.040, 56.040, 205.068
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein SmbA


Mass: 32039.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides CB15 (bacteria) / Strain: ATCC 19089 / CB15 / Gene: CC_2504 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9A5E6

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Non-polymers , 5 types, 317 molecules

#2: Chemical ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate


Mass: 690.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N10O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2M CaCl2, 0.1M Tris pH 8.0, 20% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→21.53 Å / Num. obs: 65594 / % possible obs: 99.93 % / Redundancy: 22.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.021 / Net I/σ(I): 20.6
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 22.9 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 6381 / CC1/2: 0.78 / % possible all: 99.87

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.12-2829-000refinement
MOSFLMdata reduction
MOLREPphasing
PDB_EXTRACT3.27data extraction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GS8

6gs8


Resolution: 1.4→21.523 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 14.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1773 3326 5.07 %
Rwork0.148 62268 -
obs0.1494 65594 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.7 Å2 / Biso mean: 20.7039 Å2 / Biso min: 7 Å2
Refinement stepCycle: final / Resolution: 1.4→21.523 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2081 0 129 299 2509
Biso mean--29.06 33.31 -
Num. residues----270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062209
X-RAY DIFFRACTIONf_angle_d0.8982987
X-RAY DIFFRACTIONf_chiral_restr0.072329
X-RAY DIFFRACTIONf_plane_restr0.005416
X-RAY DIFFRACTIONf_dihedral_angle_d19.697828
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.4-1.41990.24411360.20562516
1.4199-1.44110.23581580.18062550
1.4411-1.46360.21821300.16532532
1.4636-1.48760.211340.16042539
1.4876-1.51320.2021390.15172572
1.5132-1.54070.18831400.14932528
1.5407-1.57030.18961370.13992561
1.5703-1.60240.17281300.13222576
1.6024-1.63720.17361380.12632535
1.6372-1.67530.1661470.12052538
1.6753-1.71720.17381420.11942586
1.7172-1.76360.17221250.12012584
1.7636-1.81540.16791430.11622556
1.8154-1.8740.13141350.12082580
1.874-1.94090.16351260.11782591
1.9409-2.01860.14221230.12012611
2.0186-2.11040.16351270.12532582
2.1104-2.22150.1691490.12972604
2.2215-2.36060.15351370.13092615
2.3606-2.54260.15231500.14412608
2.5426-2.79790.17231470.15422643
2.7979-3.20170.18111390.16242664
3.2017-4.02940.16471330.16072728
4.0294-21.520.22521610.18322869

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