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- PDB-1fx4: STRUCTURE ANALYSIS OF ADENYLATE CYCLASES FROM TRYPANOSOMA BRUCEI ... -

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Basic information

Entry
Database: PDB / ID: 1fx4
TitleSTRUCTURE ANALYSIS OF ADENYLATE CYCLASES FROM TRYPANOSOMA BRUCEI IN THEIR MONOMERIC STATE
ComponentsRECEPTOR-TYPE ADENYLATE CYCLASE GRESAG 4.3
KeywordsLYASE / adenylyl cyclases / catalysis / trypanosomes / monomer-dimer / magnesium
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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Receptor-type adenylate cyclase GRESAG 4.3
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 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 1.3Jan 31, 2018Group: Advisory / Experimental preparation / Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 4.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9092
Polymers25,8851
Non-polymers241
Water4,756264
1
A: RECEPTOR-TYPE ADENYLATE CYCLASE GRESAG 4.3
hetero molecules

A: RECEPTOR-TYPE ADENYLATE CYCLASE GRESAG 4.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8194
Polymers51,7702
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554-y+1/2,x,z-1/41
Unit cell
Length a, b, c (Å)90.000, 90.000, 66.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein RECEPTOR-TYPE ADENYLATE CYCLASE GRESAG 4.3 / ATP PYROPHOSPHATE-LYASE / ADENYLYL CYCLASE


Mass: 25884.969 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: Q99280, adenylate cyclase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7
Details: 20 mM Tris/HCl, 25 % PEG 4000, 0.2 M MgCl2, pH 7.0, 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
335 %(w/v)PEG40001reservoir
40.2 M1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.07
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 21016 / Num. obs: 21016 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 21.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5 % / Rmerge(I) obs: 0.283 / Num. unique all: 2075 / % possible all: 98.9
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 23 Å / % possible obs: 99.5 % / Num. measured all: 136749 / Rmerge(I) obs: 0.095
Reflection shell
*PLUS
% possible obs: 99.7 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 13.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementResolution: 1.9→18.67 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1841415.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 688 3.3 %RANDOM
Rwork0.202 ---
obs0.202 21016 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.05 Å2 / ksol: 0.394 e/Å3
Displacement parametersBiso mean: 32.7 Å2
Baniso -1Baniso -2Baniso -3
1--7.51 Å20 Å20 Å2
2---7.51 Å20 Å2
3---15.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.9→18.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1798 0 1 264 2063
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d1.28
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.288 127 3.6 %
Rwork0.233 3359 -
obs--99.8 %
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
X-RAY DIFFRACTION5ION.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.28
LS refinement shell
*PLUS
Rfactor Rfree: 0.288 / % reflection Rfree: 3.6 % / Rfactor Rwork: 0.233

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