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- PDB-1f5m: STRUCTURE OF THE GAF DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1f5m
TitleSTRUCTURE OF THE GAF DOMAIN
ComponentsGAF
KeywordsSIGNALING PROTEIN / GAF / cGMP binding
Function / homology
Function and homology information


L-methionine (R)-S-oxide reductase / L-methionine-(R)-S-oxide reductase activity / cellular response to oxidative stress / nucleus / cytosol / cytoplasm
Similarity search - Function
Free Met sulfoxide reductase conserved site / Uncharacterized protein family UPF0067 signature. / : / GAF domain / GAF domain / GAF domain / GAF domain / GAF-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / Free methionine-R-sulfoxide reductase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsHo, Y.S. / Burden, L.M. / Hurley, J.H.
CitationJournal: EMBO J. / Year: 2000
Title: Structure of the GAF domain, a ubiquitous signaling motif and a new class of cyclic GMP receptor.
Authors: Ho, Y.S. / Burden, L.M. / Hurley, J.H.
History
DepositionJun 15, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GAF
B: GAF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,22611
Polymers39,5072
Non-polymers7199
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-20 kcal/mol
Surface area15280 Å2
MethodPISA
2
A: GAF
B: GAF
hetero molecules

A: GAF
B: GAF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,45122
Polymers79,0134
Non-polymers1,43818
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area9250 Å2
ΔGint-46 kcal/mol
Surface area28830 Å2
MethodPISA
3
A: GAF
B: GAF
hetero molecules

A: GAF
B: GAF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,45122
Polymers79,0134
Non-polymers1,43818
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8860 Å2
ΔGint-43 kcal/mol
Surface area29220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.640, 73.640, 162.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein GAF


Mass: 19753.252 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P36088
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O
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: 2.79 Å3/Da / Density % sol: 55.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium sulfate, lithium sulfate, Tris buffer, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
250 mMTris1drop
32 mMdithiothreitol1drop
40.1 MTris-HCl1reservoir
50.2 M1reservoirLi2SO4
62.0 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.915
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 23, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.915 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 67128 / Num. obs: 36203 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 27.9
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.545 / % possible all: 99.5
Reflection
*PLUS
Num. measured all: 901143
Reflection shell
*PLUS
Highest resolution: 1.9 Å / % possible obs: 99.5 % / Mean I/σ(I) obs: 2.73

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNSrefinement
RefinementResolution: 1.9→500 Å
RfactorNum. reflection% reflectionSelection details
Rfree0.246 2788 -Random
Rwork0.214 ---
all0.246 67290 --
obs0.214 64443 95.8 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.59 Å20 Å20 Å2
2---1.59 Å20 Å2
3---3.181 Å2
Refinement stepCycle: LAST / Resolution: 1.9→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2724 0 9 346 3079
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.016334
X-RAY DIFFRACTIONx_angle_deg1.72526
X-RAY DIFFRACTIONx_mcbond_it1.5671.5
X-RAY DIFFRACTIONx_mcangle_it2.3322
X-RAY DIFFRACTIONx_scbond_it2.3622
X-RAY DIFFRACTIONx_scangle_it3.2622.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 500 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5

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