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- PDB-5d0h: Crystal Structure of triple mutant (KDA to EGY) of an adenylyl cy... -

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Basic information

Entry
Database: PDB / ID: 5d0h
TitleCrystal Structure of triple mutant (KDA to EGY) of an adenylyl cyclase Ma1120 from Mycobacterium avium in complex with ATP and calcium ion
ComponentsCyclase
KeywordsLYASE / Adenylyl cyclase / ATP
Function / homology
Function and homology information


cyclic nucleotide biosynthetic process / adenylate cyclase activity / intracellular signal transduction / GTP binding / ATP binding / membrane / 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
ADENOSINE-5'-TRIPHOSPHATE / Cyclase
Similarity search - Component
Biological speciesMycobacterium avium subsp. avium 10-9275 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBharambe, N.G. / Suguna, K.
CitationJournal: Febs J. / Year: 2016
Title: Substrate specificity determinants of class III nucleotidyl cyclases
Authors: Bharambe, N.G. / Barathy, D.V. / Syed, W. / Visweswariah, S.S. / Cola sigmaf o, M. / Misquith, S. / Suguna, K.
History
DepositionAug 3, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Nov 2, 2016Group: Database references
Revision 1.3Nov 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclase
B: Cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3376
Polymers39,2432
Non-polymers1,0954
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-42 kcal/mol
Surface area14350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.350, 46.450, 48.690
Angle α, β, γ (deg.)72.02, 82.82, 85.76
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Cyclase /


Mass: 19621.336 Da / Num. of mol.: 2 / Fragment: UNP residues 106-275 / Mutation: K153E,D209G,A219Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium subsp. avium 10-9275 (bacteria)
Gene: O972_06080 / Plasmid: pPROExHT / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: V7LAR8
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.16 Å3/Da / Density % sol: 37.74 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 7.5 / Details: 0.1M HEPES, 30% (w/v) PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54418 Å / Relative weight: 1
ReflectionResolution: 2.1→46.04 Å / Num. obs: 16726 / % possible obs: 95.4 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 4.1
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2 / % possible all: 93.3

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WP9

4wp9


Resolution: 2.1→23.542 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2577 847 5.07 %
Rwork0.2193 --
obs0.2213 16717 95.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→23.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2377 0 64 208 2649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012489
X-RAY DIFFRACTIONf_angle_d0.983366
X-RAY DIFFRACTIONf_dihedral_angle_d15.285892
X-RAY DIFFRACTIONf_chiral_restr0.035381
X-RAY DIFFRACTIONf_plane_restr0.003431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.23150.31691400.28842568X-RAY DIFFRACTION93
2.2315-2.40360.31291350.26472635X-RAY DIFFRACTION94
2.4036-2.64520.30181470.24822614X-RAY DIFFRACTION95
2.6452-3.02730.24511360.23312678X-RAY DIFFRACTION96
3.0273-3.81150.2421400.19682690X-RAY DIFFRACTION97
3.8115-23.54310.22111490.18412685X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -54.8711 Å / Origin y: 36.4523 Å / Origin z: -33.4504 Å
111213212223313233
T0.144 Å20.0047 Å20.0473 Å2-0.2223 Å20.0233 Å2--0.1523 Å2
L1.0111 °2-0.2447 °20.3686 °2-0.975 °2-0.5071 °2--1.075 °2
S0.0172 Å °-0.0076 Å °-0.0006 Å °-0.0289 Å °-0.0063 Å °-0.049 Å °0.0367 Å °0.0693 Å °-0.0104 Å °
Refinement TLS groupSelection details: all

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