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- PDB-4wp8: Crystal structure of Adenylyl cyclase Ma1120 from Mycobacterium A... -

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Basic information

Entry
Database: PDB / ID: 4wp8
TitleCrystal structure of Adenylyl cyclase Ma1120 from Mycobacterium Avium in complex with 2'5'-DD-3'-ATP and Manganese ion
ComponentsMa1120
KeywordsLYASE / Adenylyl cyclase / 2'5'-dd-3'-ATP
Function / homology
Function and homology information


cyclic nucleotide biosynthetic process / adenylate cyclase / adenylate cyclase activity / intracellular signal transduction / metal ion binding
Similarity search - Function
: / Nucleotide cyclase, GGDEF domain / 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
: / Chem-ZDA / Cya1120
Similarity search - Component
Biological speciesMycobacterium avium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBarathy, D.V. / Bharambe, N.G. / Suguna, K.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Autoinhibitory mechanism and activity-related structural changes in a mycobacterial adenylyl cyclase
Authors: Barathy, D.V. / Bharambe, N.G. / Syed, W. / Zaveri, A. / Visweswariah, S.S. / Cola sigmaf o, M. / Misquith, S. / Suguna, K.
History
DepositionOct 17, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ma1120
B: Ma1120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2578
Polymers38,1262
Non-polymers1,1316
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-28 kcal/mol
Surface area14780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.970, 55.960, 54.070
Angle α, β, γ (deg.)90.00, 106.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ma1120 / Cya1120 / Adenylyl cyclase


Mass: 19062.814 Da / Num. of mol.: 2 / Fragment: UNP residues 53-216
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium (bacteria) / Strain: TN 104 / Gene: cya1120 / Plasmid: pPROExHT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5UFR5, adenylate cyclase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ZDA / 2',5'-dideoxyadenosine 3'-(tetrahydrogen triphosphate) / 2',5'-DIDEOXYADENOSINE 3'-TRIPHOSPHATE


Mass: 475.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O11P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 1.98 Å3/Da / Density % sol: 37.84 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 9.1
Details: 0.2M Sodium phosphate dibasic dihydrate, 20 % (w/v) Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95327 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 27, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95327 Å / Relative weight: 1
ReflectionResolution: 1.65→55.96 Å / Num. obs: 35884 / % possible obs: 99.78 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 14.3
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 3.1 / % possible all: 99.5

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Processing

SoftwareName: REFMAC / Version: 5.8.0073 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WP3

4wp3


Resolution: 1.65→55.96 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.031 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21496 1792 5 %RANDOM
Rwork0.17188 ---
obs0.17401 34074 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.557 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20.95 Å2
2---0.94 Å2-0 Å2
3---0.3 Å2
Refinement stepCycle: 1 / Resolution: 1.65→55.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2415 0 60 261 2736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192624
X-RAY DIFFRACTIONr_bond_other_d0.0010.022500
X-RAY DIFFRACTIONr_angle_refined_deg1.2791.993566
X-RAY DIFFRACTIONr_angle_other_deg0.6835691
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0065349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.34522.667105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.79915431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3391528
X-RAY DIFFRACTIONr_chiral_restr0.0680.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023002
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02615
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_it1.1212.0571352
X-RAY DIFFRACTIONr_mcbond_other1.1182.0561351
X-RAY DIFFRACTIONr_mcangle_it1.8163.0691693
X-RAY DIFFRACTIONr_mcangle_other1.8163.071694
X-RAY DIFFRACTIONr_scbond_it1.6862.2081272
X-RAY DIFFRACTIONr_scbond_other1.6852.2121261
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6863.2191866
X-RAY DIFFRACTIONr_long_range_B_refined5.35717.2113131
X-RAY DIFFRACTIONr_long_range_B_other4.84716.5313006
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 132 -
Rwork0.234 2533 -
obs--99.37 %

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