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- PDB-8bvb: Crystal structure of the apo form of SmbA loop deletion mutant. -

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Basic information

Entry
Database: PDB / ID: 8bvb
TitleCrystal structure of the apo form of SmbA loop deletion mutant.
ComponentsAldo_ket_red domain-containing protein
KeywordsSIGNALING PROTEIN / c-di-GMP receptor / ppGpp / second messenger / TIM barrel
Function / homologyNADP-dependent oxidoreductase domain / NADP-dependent oxidoreductase domain superfamily / nucleotide binding / TIM Barrel / Alpha-Beta Barrel / metal ion binding / Alpha Beta / NADP-dependent oxidoreductase domain-containing protein
Function and homology information
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDubey, B.N. / Schirmer, T.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_166652 Switzerland
CitationJournal: Sci Rep / Year: 2023
Title: Mutant structure of metabolic switch protein in complex with monomeric c-di-GMP reveals a potential mechanism of protein-mediated ligand dimerization.
Authors: Dubey, B.N. / Shyp, V. / Fucile, G. / Sondermann, H. / Jenal, U. / Schirmer, T.
History
DepositionDec 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / refine
Item: _pdbx_initial_refinement_model.type / _refine.pdbx_starting_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aldo_ket_red domain-containing protein
B: Aldo_ket_red domain-containing protein
C: Aldo_ket_red domain-containing protein
D: Aldo_ket_red domain-containing protein


Theoretical massNumber of molelcules
Total (without water)128,0844
Polymers128,0844
Non-polymers00
Water22,8791270
1
A: Aldo_ket_red domain-containing protein
B: Aldo_ket_red domain-containing protein

D: Aldo_ket_red domain-containing protein

C: Aldo_ket_red domain-containing protein


Theoretical massNumber of molelcules
Total (without water)128,0844
Polymers128,0844
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_656x+1,y,z+11
crystal symmetry operation1_655x+1,y,z1
Buried area13890 Å2
ΔGint-51 kcal/mol
Surface area48190 Å2
Unit cell
Length a, b, c (Å)61.375, 208.105, 64.234
Angle α, β, γ (deg.)90.000, 117.575, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Aldo_ket_red domain-containing protein


Mass: 32021.057 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Strain: NA 1000 / Gene: CC_2504 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3 / References: UniProt: Q9A5E6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1270 / 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: 2.84 Å3/Da / Density % sol: 56.67 %
Crystal growTemperature: 303 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 200 mM NaCl and 10 % v/w PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97319 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97319 Å / Relative weight: 1
ReflectionResolution: 1.8→56.94 Å / Num. obs: 128620 / % possible obs: 97.84 % / Redundancy: 3.3 % / Biso Wilson estimate: 20.39 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.07474 / Rpim(I) all: 0.04879 / Rrim(I) all: 0.08954 / Net I/σ(I): 12.06
Reflection shellResolution: 1.8→1.864 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.5554 / Mean I/σ(I) obs: 2.86 / Num. unique obs: 12871 / CC1/2: 0.763 / CC star: 0.93 / Rpim(I) all: 0.3609 / Rrim(I) all: 0.6642 / % possible all: 97.84

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Processing

Software
NameVersionClassification
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PHENIX1.19.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GS8

6gs8


Resolution: 1.8→56.94 Å / SU ML: 0.2002 / Cross valid method: FREE R-VALUE / σ(F): 0.94 / Phase error: 21.0485
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2031 6163 4.79 %
Rwork0.1689 122435 -
obs0.1706 128598 97.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.65 Å2
Refinement stepCycle: LAST / Resolution: 1.8→56.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8952 0 0 1270 10222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00929132
X-RAY DIFFRACTIONf_angle_d1.051312392
X-RAY DIFFRACTIONf_chiral_restr0.0621368
X-RAY DIFFRACTIONf_plane_restr0.011652
X-RAY DIFFRACTIONf_dihedral_angle_d5.37771272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.28312230.24614035X-RAY DIFFRACTION97.89
1.82-1.840.28912340.23734071X-RAY DIFFRACTION98
1.84-1.860.29642180.23664090X-RAY DIFFRACTION97.64
1.86-1.890.26662100.24384034X-RAY DIFFRACTION97.68
1.89-1.910.34972040.254100X-RAY DIFFRACTION97.62
1.91-1.940.29171950.24054039X-RAY DIFFRACTION98.26
1.94-1.970.24382260.21284061X-RAY DIFFRACTION97.77
1.97-20.26561770.19844144X-RAY DIFFRACTION98.43
2-2.030.24261990.18774078X-RAY DIFFRACTION97.96
2.03-2.060.21472090.17854102X-RAY DIFFRACTION98.25
2.06-2.10.23782030.17994064X-RAY DIFFRACTION97.53
2.1-2.130.21452360.18074013X-RAY DIFFRACTION97.9
2.13-2.180.23492440.17574065X-RAY DIFFRACTION98
2.18-2.220.21982130.17984117X-RAY DIFFRACTION98.84
2.22-2.270.21511970.17694105X-RAY DIFFRACTION98.22
2.27-2.320.2331610.18324157X-RAY DIFFRACTION98.47
2.32-2.380.22781810.1864128X-RAY DIFFRACTION98.47
2.38-2.440.2411710.1754131X-RAY DIFFRACTION98.35
2.44-2.510.21351940.16774077X-RAY DIFFRACTION98.18
2.51-2.60.18532210.16784096X-RAY DIFFRACTION97.89
2.6-2.690.21561840.16674110X-RAY DIFFRACTION98.08
2.69-2.80.21461830.16424142X-RAY DIFFRACTION98.36
2.8-2.920.20052130.16054102X-RAY DIFFRACTION98.25
2.92-3.080.19452310.16214048X-RAY DIFFRACTION97.72
3.08-3.270.20251970.16274033X-RAY DIFFRACTION97.2
3.27-3.520.18792360.14883941X-RAY DIFFRACTION95.76
3.52-3.880.16172050.14384046X-RAY DIFFRACTION96.33
3.88-4.440.17171920.13464098X-RAY DIFFRACTION97.63
4.44-5.590.14692290.14334054X-RAY DIFFRACTION97.19
5.59-56.940.16581770.16754154X-RAY DIFFRACTION97.35

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