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- PDB-4p2x: Swapped Dimer of Mycobacterial Adenylyl cyclase Rv1625c: Form 2 -

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Basic information

Entry
Database: PDB / ID: 4p2x
TitleSwapped Dimer of Mycobacterial Adenylyl cyclase Rv1625c: Form 2
ComponentsAdenylate cyclase
KeywordsLYASE / Adenylyl Cyclase / beta-alpha-beta sandwich / Domain swapping / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 5, 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_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / 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_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _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

Downloads & links

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Assembly

Deposited unit
A: Adenylate cyclase
B: Adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8099
Polymers57,2282
Non-polymers5807
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7830 Å2
ΔGint-65 kcal/mol
Surface area17620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.570, 75.570, 133.170
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
DetailsDimer in solution confirmed by gel filtration

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 28614.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: cya, Rv1625c, MT1661, MTCY01B2.17c / Plasmid: P-PROEXHT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P0A4Y0, UniProt: P9WQ35*PLUS, adenylate cyclase

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Non-polymers , 5 types, 60 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35.87 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 8.5 / Details: 0.2M Lithium sulphate, Tris pH 8.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978565 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 1, 2013 / Details: bent collimating mirror and toroid
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 2.4→37.78 Å / Num. obs: 16832 / % possible obs: 99.8 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 23.5
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 4.9 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
SCALAccp4 6.3data scaling
iMOSFLM1.0.7data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4P2M

4p2m


Resolution: 2.4→36.76 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.909 / SU B: 7.476 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.334 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25957 849 5 %RANDOM
Rwork0.19623 ---
obs0.19925 15982 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.313 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å2-0.33 Å20 Å2
2---0.33 Å20 Å2
3---1.07 Å2
Refinement stepCycle: 1 / Resolution: 2.4→36.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2535 0 35 53 2623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192622
X-RAY DIFFRACTIONr_bond_other_d0.0010.022509
X-RAY DIFFRACTIONr_angle_refined_deg1.1511.9543555
X-RAY DIFFRACTIONr_angle_other_deg0.70535728
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.615333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.39123.684114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.87315375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1281518
X-RAY DIFFRACTIONr_chiral_restr0.0660.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212971
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02587
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: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 61 -
Rwork0.219 1185 -
obs--99.52 %

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