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- PDB-5d15: Crystal structure of an adenylyl cyclase Ma1120 from Mycobacteriu... -

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Basic information

Entry
Database: PDB / ID: 5d15
TitleCrystal structure 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 / metal ion binding / membrane
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
ADENOSINE-5'-TRIPHOSPHATE / Cyclase
Similarity search - Component
Biological speciesMycobacterium avium subsp. avium 10-9275 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBharambe, N.G. / Barathy, D.V. / 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 / struct_conn_type
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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_conn_type.id
Revision 1.4Sep 17, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact ...pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclase
B: Cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3317
Polymers39,1752
Non-polymers1,1575
Water5,927329
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-33 kcal/mol
Surface area14090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.530, 55.640, 55.070
Angle α, β, γ (deg.)90.00, 109.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cyclase


Mass: 19587.342 Da / Num. of mol.: 2 / Fragment: UNP residues 106-275
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


Mass: 507.181 Da / Num. of mol.: 2 / Source method: isolated from a natural source / 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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 36.37 %
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: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 12, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.5→37.92 Å / Num. obs: 47922 / % possible obs: 100 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 8.1
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: 1.10pre_2084 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WP9

4wp9


Resolution: 1.5→37.92 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2117 2338 4.89 %
Rwork0.1951 --
obs0.1959 47798 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→37.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2377 0 68 329 2774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0322653
X-RAY DIFFRACTIONf_angle_d1.2893583
X-RAY DIFFRACTIONf_dihedral_angle_d20.271958
X-RAY DIFFRACTIONf_chiral_restr0.043406
X-RAY DIFFRACTIONf_plane_restr0.006458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53060.34781610.31442629X-RAY DIFFRACTION100
1.5306-1.56390.31611380.29822657X-RAY DIFFRACTION100
1.5639-1.60030.28611420.27612681X-RAY DIFFRACTION100
1.6003-1.64030.28461460.26092638X-RAY DIFFRACTION100
1.6403-1.68470.27481300.26592667X-RAY DIFFRACTION100
1.6847-1.73420.30121340.24492691X-RAY DIFFRACTION100
1.7342-1.79020.23981430.23032653X-RAY DIFFRACTION100
1.7902-1.85420.25431370.22752682X-RAY DIFFRACTION100
1.8542-1.92840.27911230.27422639X-RAY DIFFRACTION99
1.9284-2.01620.26141450.21222665X-RAY DIFFRACTION100
2.0162-2.12250.21031350.19832701X-RAY DIFFRACTION100
2.1225-2.25540.24421330.20622636X-RAY DIFFRACTION99
2.2554-2.42960.22361170.18922678X-RAY DIFFRACTION99
2.4296-2.6740.20521230.18442714X-RAY DIFFRACTION100
2.674-3.06080.21041430.18232690X-RAY DIFFRACTION100
3.0608-3.85570.181470.16022699X-RAY DIFFRACTION100
3.8557-37.9320.15361410.16462740X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.7535-1.75950.37472.2058-0.0251.71820.1123-0.24870.25610.1294-0.07120.1481-0.3096-0.2544-0.02660.21970.0060.03210.12450.02180.102926.6156-39.2574113.4896
22.75330.1269-0.62672.8163-0.02872.81120.0463-0.20110.070.23640.0098-0.0638-0.1471-0.0201-0.03680.1235-0.0048-0.00890.0821-0.00360.08236.0881-47.7608113.7356
33.74520.83642.08934.6130.88175.07130.1875-0.2773-0.20270.2957-0.02380.02790.2389-0.2604-0.10560.15740.01060.00460.11270.04090.169633.9196-60.6445115.3466
48.5422-3.6406-3.05456.68024.43099.00270.3648-0.38890.32580.0517-0.08390.2508-0.6133-0.1423-0.19450.2006-0.02940.0190.16590.03060.158219.6175-36.176495.9812
56.4261-7.13493.53579.0197-4.25712.53250.43670.3276-0.9518-0.5426-0.05390.54740.277-0.164-0.30610.2203-0.0024-0.02950.1689-0.00310.154735.104-56.486593.9812
67.6243-6.68174.49539.0525-5.55325.78780.04520.25970.3515-0.4913-0.0526-0.2687-0.04080.146-0.03110.2278-0.03860.03080.17950.00120.129935.996-41.933488.2052
72.5446-2.8447-0.17835.9558-0.11313.59280.1469-0.430.38870.57180.1506-0.4239-0.37570.342-0.16540.2997-0.0527-0.02060.26510.02590.25226.7004-36.073393.8743
84.9301-4.9632-2.08065.64282.77973.03650.22920.8141-0.0672-0.8220.02330.0636-0.3102-0.1416-0.15440.3209-0.0161-0.03260.28080.01810.185423.9251-41.326981.7401
94.6071-1.5718-1.55056.63222.26835.83650.10550.2157-0.0422-0.2528-0.06560.2099-0.26660.1203-0.060.1142-0.02-0.02310.12130.05430.113321.3833-41.27592.7021
102.1494-1.9766-0.91883.90380.93495.301-0.03490.0073-0.13750.07970.11170.3707-0.171-0.169-0.05490.11310.0091-0.00970.14260.03670.222415.5733-40.92294.8512
114.27640.05990.56492.6823-0.79128.06260.05770.5278-0.2842-0.3610.21960.45550.1267-0.6272-0.290.16390.0139-0.07990.2709-0.00620.34919.331-45.314989.5602
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 102 through 147 )
2X-RAY DIFFRACTION2chain 'A' and (resid 148 through 244 )
3X-RAY DIFFRACTION3chain 'A' and (resid 245 through 271 )
4X-RAY DIFFRACTION4chain 'B' and (resid 103 through 114 )
5X-RAY DIFFRACTION5chain 'B' and (resid 115 through 125 )
6X-RAY DIFFRACTION6chain 'B' and (resid 126 through 147 )
7X-RAY DIFFRACTION7chain 'B' and (resid 148 through 165 )
8X-RAY DIFFRACTION8chain 'B' and (resid 166 through 183 )
9X-RAY DIFFRACTION9chain 'B' and (resid 184 through 206 )
10X-RAY DIFFRACTION10chain 'B' and (resid 207 through 240 )
11X-RAY DIFFRACTION11chain 'B' and (resid 241 through 271 )

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