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- PDB-1fx2: STRUCTURAL ANALYSIS OF ADENYLATE CYCLASES FROM TRYPANOSOMA BRUCEI... -

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Basic information

Entry
Database: PDB / ID: 1fx2
TitleSTRUCTURAL ANALYSIS OF ADENYLATE CYCLASES FROM TRYPANOSOMA BRUCEI IN THEIR MONOMERIC STATE
ComponentsRECEPTOR-TYPE ADENYLATE CYCLASE GRESAG 4.1
KeywordsLYASE / cAMP / trypanosomes / adenylyl cyclases / monomer-dimer / catalysis
Function / homology
Function and homology information


adenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / membrane => GO:0016020 / intracellular signal transduction / ATP binding / metal ion binding
Similarity search - Function
Nucleotide cyclase, GGDEF domain / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Nucleotide cyclase / Periplasmic binding protein-like I / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Receptor-type adenylate cyclase GRESAG 4.1
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.46 Å
AuthorsBieger, B. / Essen, L.-O.
CitationJournal: EMBO J. / Year: 2001
Title: Structural analysis of adenylate cyclases from Trypanosoma brucei in their monomeric state.
Authors: Bieger, B. / Essen, L.O.
History
DepositionSep 25, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _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: RECEPTOR-TYPE ADENYLATE CYCLASE GRESAG 4.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7553
Polymers26,5051
Non-polymers2502
Water4,900272
1
A: RECEPTOR-TYPE ADENYLATE CYCLASE GRESAG 4.1
hetero molecules

A: RECEPTOR-TYPE ADENYLATE CYCLASE GRESAG 4.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5106
Polymers53,0092
Non-polymers5014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x+1/2,-y+3/2,-z1
Unit cell
Length a, b, c (Å)49.600, 60.070, 78.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly in the catalytic state is a dimer

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Components

#1: Protein RECEPTOR-TYPE ADENYLATE CYCLASE GRESAG 4.1


Mass: 26504.740 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Strain: STRAIN 927 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / References: UniProt: Q99279, adenylate cyclase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.22 Å3/Da / Density % sol: 44.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: 20 mM Tris/HCl, 1.8-1.9 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, temperature 18K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
25 mMTris-HCl1drop
325 %(w/v)PEG40001reservoir
40.2 M1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.833
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 8, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.833 Å / Relative weight: 1
ReflectionResolution: 1.46→10 Å / Num. all: 498167 / Num. obs: 40911 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 24.7
Reflection shellResolution: 1.44→1.48 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.283 / Num. unique all: 2799 / % possible all: 98.9
Reflection
*PLUS
Num. measured all: 498167
Reflection shell
*PLUS
% possible obs: 98.9 % / Mean I/σ(I) obs: 4.3

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Processing

Software
NameVersionClassification
SHARPphasing
SOLOMONphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.46→10 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1440982.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1111 2.8 %RANDOM
Rwork0.178 ---
obs0.178 39779 95.7 %-
all-498167 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.42 Å2 / ksol: 0.431 e/Å3
Displacement parametersBiso mean: 20.1 Å2
Baniso -1Baniso -2Baniso -3
1-6.32 Å20 Å20 Å2
2---2.98 Å20 Å2
3----3.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.46→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1894 0 13 272 2179
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.031
X-RAY DIFFRACTIONc_angle_deg2.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d2.26
X-RAY DIFFRACTIONc_mcbond_it2.961.5
X-RAY DIFFRACTIONc_mcangle_it4.232
X-RAY DIFFRACTIONc_scbond_it6.062
X-RAY DIFFRACTIONc_scangle_it7.562.5
LS refinement shellResolution: 1.46→1.55 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.264 165 2.6 %
Rwork0.222 6135 -
obs--92.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DTT.PARAMDTT.TOP
X-RAY DIFFRACTION3PARAM.PO4TOP.PO4
X-RAY DIFFRACTION4WATER.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 2.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg2.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.26
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.264 / % reflection Rfree: 2.6 % / Rfactor Rwork: 0.222

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