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- PDB-8egk: Re-refinement of Crystal Structure of NosGet3d, the All4481 prote... -

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Basic information

Entry
Database: PDB / ID: 8egk
TitleRe-refinement of Crystal Structure of NosGet3d, the All4481 protein from Nostoc sp. PCC 7120
ComponentsAll4481 protein
KeywordsCHAPERONE / P-loop ATPase / Get3 / alpha-crystallin / cyanobacteria
Function / homologyArsA, HSP20-like domain / : / HSP20-like domain found in ArsA / Anion-transporting ATPase-like domain / Anion-transporting ATPase / HSP20-like chaperone / P-loop containing nucleoside triphosphate hydrolase / AZIDE ION / All4481 protein
Function and homology information
Biological speciesNostoc sp. PCC 7120 = FACHB-418 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.98 Å
AuthorsBarlow, A.N. / Manu, M.S. / Ramasamy, S. / Clemons Jr., W.M.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorR01GM097572 United States
National Institutes of Health/Office of the DirectorR01GM125063 United States
National Institutes of Health/Office of the DirectorDP1GM105385 United States
Other privateWeston Havens Foundation
National Science Foundation (NSF, United States)11444469 United States
National Institutes of Health/Office of the DirectorT32GM07616 United States
Citation
Journal: J.Biol.Chem. / Year: 2023
Title: Structures of Get3d reveal a distinct architecture associated with the emergence of photosynthesis.
Authors: Barlow, A.N. / Manu, M.S. / Saladi, S.M. / Tarr, P.T. / Yadav, Y. / Thinn, A.M.M. / Zhu, Y. / Laganowsky, A.D. / Clemons Jr., W.M. / Ramasamy, S.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Liebschner, D. / Afonine, P.V. / Baker, M.L. / Bunkoczi, G. / Chen, V.B. / Croll, T.I. / Hintze, B. / Hung, L.W. / Jain, S. / McCoy, A.J. / Moriarty, N.W. / Oeffner, R.D. / Poon, B.K. / ...Authors: Liebschner, D. / Afonine, P.V. / Baker, M.L. / Bunkoczi, G. / Chen, V.B. / Croll, T.I. / Hintze, B. / Hung, L.W. / Jain, S. / McCoy, A.J. / Moriarty, N.W. / Oeffner, R.D. / Poon, B.K. / Prisant, M.G. / Read, R.J. / Richardson, J.S. / Richardson, D.C. / Sammito, M.D. / Sobolev, O.V. / Stockwell, D.H. / Terwilliger, T.C. / Urzhumtsev, A.G. / Videau, L.L. / Williams, C.J. / Adams, P.D.
History
DepositionSep 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 25, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: All4481 protein
B: All4481 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2504
Polymers83,1662
Non-polymers842
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7140 Å2
ΔGint-47 kcal/mol
Surface area31250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.170, 55.553, 122.363
Angle α, β, γ (deg.)90.000, 98.870, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein All4481 protein


Mass: 41582.953 Da / Num. of mol.: 2 / Mutation: A127T
Source method: isolated from a genetically manipulated source
Details: C-terminal His6 purification tag
Source: (gene. exp.) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: all4481 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YNT0
#2: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.65 Å3/Da / Density % sol: 53.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.15
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Reservoir solution: 100mM MES (pH 6.15), 18% PEG3350, and 100mM potassium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97908 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 14, 2009
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 1.98→27.52 Å / Num. obs: 110202 / % possible obs: 89.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 28.11 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 18.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.288 / Num. unique obs: 11087 / Rsym value: 0.28

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
REFMACUnknownrefinement
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SnBphasing
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3IGF

3igf


Resolution: 1.98→27.52 Å / SU ML: 0.1692 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 21.2305
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2209 2621 4.84 %
Rwork0.1889 51541 -
obs0.1905 54162 94.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.26 Å2
Refinement stepCycle: LAST / Resolution: 1.98→27.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5528 0 6 339 5873
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075644
X-RAY DIFFRACTIONf_angle_d0.7587682
X-RAY DIFFRACTIONf_chiral_restr0.0493902
X-RAY DIFFRACTIONf_plane_restr0.0147992
X-RAY DIFFRACTIONf_dihedral_angle_d5.4395756
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.020.2896850.20692099X-RAY DIFFRACTION73.41
2.02-2.060.22941290.20382688X-RAY DIFFRACTION92.73
2.06-2.10.26481470.19622612X-RAY DIFFRACTION93.46
2.1-2.150.23521370.19252725X-RAY DIFFRACTION94.11
2.15-2.20.24931230.20362646X-RAY DIFFRACTION92.73
2.2-2.250.33261280.26082393X-RAY DIFFRACTION84.63
2.25-2.310.27361250.20982453X-RAY DIFFRACTION85
2.31-2.380.22581450.18492698X-RAY DIFFRACTION95.56
2.38-2.460.17111590.17732765X-RAY DIFFRACTION97.4
2.46-2.540.26841380.18012819X-RAY DIFFRACTION97.69
2.54-2.650.20171360.18312839X-RAY DIFFRACTION98.54
2.65-2.770.2051310.19342813X-RAY DIFFRACTION97.77
2.77-2.910.21651540.18772830X-RAY DIFFRACTION98.64
2.91-3.090.2341560.19152847X-RAY DIFFRACTION98.95
3.09-3.330.22911540.1992813X-RAY DIFFRACTION99.3
3.33-3.670.21841220.18282776X-RAY DIFFRACTION95.27
3.67-4.20.19271540.18112861X-RAY DIFFRACTION98.63
4.2-5.280.18831450.16672915X-RAY DIFFRACTION99.61
5.28-27.520.23241530.19432949X-RAY DIFFRACTION98.54

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