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- PDB-4p2f: Monomeric form of a single mutant (F363R) of Mycobacterial Adenyl... -

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Basic information

Entry
Database: PDB / ID: 4p2f
TitleMonomeric form of a single mutant (F363R) of Mycobacterial Adenylyl cyclase Rv1625c
ComponentsAdenylate cyclase
KeywordsLYASE / Adenylyl cyclase / Single mutant / alpha/beta fold / Signal transduction
Function / homology
Function and homology information


receptor guanylyl cyclase signaling pathway / peptide receptor activity / cGMP biosynthetic process / guanylate cyclase activity / adenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / membrane => GO:0016020 / manganese ion binding / intracellular signal transduction ...receptor guanylyl cyclase signaling pathway / peptide receptor activity / cGMP biosynthetic process / guanylate cyclase activity / adenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / membrane => GO:0016020 / manganese ion binding / intracellular signal transduction / magnesium ion binding / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
: / MASE7 / : / Nucleotide cyclase, GGDEF domain / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylate and Guanylate cyclase catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Guanylate cyclase domain profile. ...: / MASE7 / : / Nucleotide cyclase, GGDEF domain / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylate and Guanylate cyclase catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Guanylate cyclase domain profile. / Nucleotide cyclase / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Adenylate cyclase / Adenylate cyclase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsBarathy, D.V. / Mattoo, R. / Visweswariah, S.S. / Suguna, K.
CitationJournal: Iucrj / Year: 2014
Title: New structural forms of a mycobacterial adenylyl cyclase Rv1625c.
Authors: Barathy, D. / Mattoo, R. / Visweswariah, S. / Suguna, K.
History
DepositionMar 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,30521
Polymers29,9901
Non-polymers1,31520
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint52 kcal/mol
Surface area10170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.890, 67.370, 101.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsGel filtration indicates dimer in solution

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Components

#1: Protein Adenylate cyclase / ATP pyrophosphate-lyase / Adenylyl cyclase


Mass: 29989.650 Da / Num. of mol.: 1 / Mutation: F363R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: cya, Rv1625c, MT1661, MTCY01B2.17c / Plasmid: pRSET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P0A4Y0, UniProt: P9WQ35*PLUS, adenylate cyclase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.17 Å3/Da / Density % sol: 43.47 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 5.5
Details: 0.15M Ammonium sulphate, 0.1M Bis-Tris pH 5.5, 30% PEG 10K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.05→40.58 Å / Num. obs: 12712 / % possible obs: 98.98 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 19.8
Reflection shellResolution: 2.05→2.103 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 4.3 / % possible all: 97.65

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Processing

SoftwareName: REFMAC / Version: 5.7.0029 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ET6.

3et6


Resolution: 2.05→40.58 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.071 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23331 663 5 %RANDOM
Rwork0.17918 ---
obs0.18176 12712 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.873 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å20 Å2
2---0.48 Å2-0 Å2
3---1.23 Å2
Refinement stepCycle: 1 / Resolution: 2.05→40.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1445 0 85 92 1622
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191549
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7281.982065
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2115190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.87723.42970
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09615232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0671514
X-RAY DIFFRACTIONr_chiral_restr0.1330.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211157
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 43 -
Rwork0.218 914 -
obs--97.65 %

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