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- PDB-5d0g: Crystal structure of triple mutant (KDA to EGY) of adenylyl cycla... -

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Basic information

Entry
Database: PDB / ID: 5d0g
TitleCrystal structure of triple mutant (KDA to EGY) of adenylyl cyclase Ma1120 from Mycobacterium avium in complex with GTP and calcium ion
ComponentsCyclase
KeywordsLYASE / Adenylyl cyclase / GTP
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
GUANOSINE-5'-TRIPHOSPHATE / Cyclase
Similarity search - Component
Biological speciesMycobacterium avium subsp. avium 10-9275 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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)40,3696
Polymers39,2432
Non-polymers1,1274
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-41 kcal/mol
Surface area13160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.070, 55.630, 55.140
Angle α, β, γ (deg.)90.00, 108.67, 90.00
Int Tables number4
Space group name H-MP1211

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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-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, 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


Mass: 18.015 Da / Num. of mol.: 224 / 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: 1.93 Å3/Da / Density % sol: 36.2 %
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: Nov 28, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.6→38.081 Å / Num. obs: 39208 / % possible obs: 99.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 10.2
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.7 / % possible all: 98.6

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Processing

SoftwareName: PHENIX / Version: 1.10PRE_2084 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WP9

4wp9


Resolution: 1.6→38.081 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.214 1917 4.89 %
Rwork0.1887 --
obs0.19 39165 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→38.081 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2289 0 66 224 2579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112415
X-RAY DIFFRACTIONf_angle_d1.2683263
X-RAY DIFFRACTIONf_dihedral_angle_d20.6151413
X-RAY DIFFRACTIONf_chiral_restr0.275376
X-RAY DIFFRACTIONf_plane_restr0.005410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.3411620.31672579X-RAY DIFFRACTION98
1.64-1.68440.36661310.28842638X-RAY DIFFRACTION98
1.6844-1.73390.28211360.26392619X-RAY DIFFRACTION98
1.7339-1.78990.24641260.22882652X-RAY DIFFRACTION99
1.7899-1.85390.25631400.21842635X-RAY DIFFRACTION99
1.8539-1.92810.24641430.22382623X-RAY DIFFRACTION99
1.9281-2.01580.21621280.18662656X-RAY DIFFRACTION99
2.0158-2.12210.27761420.18912663X-RAY DIFFRACTION99
2.1221-2.2550.2161150.19072674X-RAY DIFFRACTION99
2.255-2.42910.19321410.17192654X-RAY DIFFRACTION99
2.4291-2.67350.22321080.17792705X-RAY DIFFRACTION100
2.6735-3.06020.21131410.18642708X-RAY DIFFRACTION100
3.0602-3.8550.18371560.17692679X-RAY DIFFRACTION100
3.855-38.09140.17841480.16282763X-RAY DIFFRACTION100
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)
13.73121.3294-0.05742.47040.38391.63770.0926-0.17530.23040.2405-0.0657-0.1171-0.1324-0.0413-0.02860.201-0.0055-0.01280.1629-0.00350.129298.4041-0.084363.3933
23.25750.4311-0.87353.1308-0.67514.5040.0385-0.5415-0.09640.6324-0.0837-0.2959-0.2633-0.13430.0250.2624-0.0136-0.08690.27210.02230.219105.9133-0.223669.1413
32.70040.21690.59781.2953-0.98493.63630.0142-0.19-0.28270.1672-0.0556-0.3026-0.09760.14080.00570.1788-0.035-0.0460.18190.03420.3134112.11150.970460.1144
43.7913-0.00110.43422.06120.15064.4570.2223-0.428-0.74590.30660.0834-0.43090.12870.3633-0.29920.2427-0.0504-0.10730.32410.0850.5622118.8336-4.015365.079
55.84971.73930.91832.5730.13831.11480.0040.10530.2171-0.0348-0.00040.0262-0.13280.0774-0.00650.1613-0.00340.02830.14410.00530.095198.34761.732343.1062
62.344-0.1697-0.38832.1489-0.28662.82360.00410.1563-0.0047-0.05950.01180.0914-0.0970.0072-0.01790.1383-0.00790.010.1229-0.00470.102291.9871-8.024641.8858
73.36350.20860.87853.6856-0.24251.94990.17220.2847-0.2318-0.3365-0.0616-0.01160.49810.0941-0.13740.18570.01820.01050.1446-0.02420.137193.2178-18.977440.1705
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 102 through 165 )
2X-RAY DIFFRACTION2chain 'A' and (resid 166 through 203 )
3X-RAY DIFFRACTION3chain 'A' and (resid 204 through 240 )
4X-RAY DIFFRACTION4chain 'A' and (resid 241 through 269 )
5X-RAY DIFFRACTION5chain 'B' and (resid 103 through 165 )
6X-RAY DIFFRACTION6chain 'B' and (resid 166 through 240 )
7X-RAY DIFFRACTION7chain 'B' and (resid 241 through 269 )

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