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

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Basic information

Entry
Database: PDB / ID: 4wpa
TitleCrystal structure of Adenylyl cyclase Ma1120 from Mycobacterium Avium bound to Pyrophosphate and Calcium
ComponentsMa1120
KeywordsLYASE / Adenylyl Cyclase / pyrophosphate
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 / 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
PYROPHOSPHATE / Cya1120
Similarity search - Component
Biological speciesMycobacterium avium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBharambe, N.G. / Barathy, D.V. / 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_conn_angle / 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_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _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

Downloads & links

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Assembly

Deposited unit
A: Ma1120
B: Ma1120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5626
Polymers38,1262
Non-polymers4364
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-46 kcal/mol
Surface area14420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.720, 55.720, 55.330
Angle α, β, γ (deg.)90.00, 110.22, 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5UFR5, adenylate cyclase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PPV / PYROPHOSPHATE / Pyrophosphate


Mass: 177.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4O7P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 325 / 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 Å3/Da / Density % sol: 38.51 %
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 29, 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: 1.7→49.47 Å / Num. obs: 33241 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 10.4
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WP8

4wp8


Resolution: 1.7→37.985 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2244 1627 4.9 %
Rwork0.1879 --
obs0.1897 33209 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→37.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2347 0 20 325 2692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012475
X-RAY DIFFRACTIONf_angle_d1.0543344
X-RAY DIFFRACTIONf_dihedral_angle_d14.102908
X-RAY DIFFRACTIONf_chiral_restr0.041384
X-RAY DIFFRACTIONf_plane_restr0.005438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7001-1.75010.32721310.29022596X-RAY DIFFRACTION100
1.7501-1.80660.32391560.26282603X-RAY DIFFRACTION100
1.8066-1.87120.22781370.23722621X-RAY DIFFRACTION100
1.8712-1.94610.31391430.25332589X-RAY DIFFRACTION100
1.9461-2.03470.21571200.1882634X-RAY DIFFRACTION100
2.0347-2.14190.22721320.18352643X-RAY DIFFRACTION100
2.1419-2.27610.22911390.18932607X-RAY DIFFRACTION100
2.2761-2.45180.21021330.18042638X-RAY DIFFRACTION100
2.4518-2.69850.22771180.18082654X-RAY DIFFRACTION100
2.6985-3.08880.21361620.18352637X-RAY DIFFRACTION100
3.0888-3.8910.21461340.16782637X-RAY DIFFRACTION100
3.891-37.99490.19511220.17342723X-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)
14.6785-1.72230.01172.3736-0.07172.1214-0.0073-0.32260.18440.26440.0530.0104-0.2527-0.1117-0.05180.2335-0.00830.02370.1565-0.00710.140429.109-39.9385115.0405
22.12590.2563-0.11852.51890.11752.68070.0503-0.1598-0.12270.23890.00060.05750.11360.0114-0.02560.16230.0074-0.00880.14990.01040.143734.8531-53.5223112.4271
32.7456-1.25610.32242.516-1.56481.7480.0512-0.05910.0538-0.3468-0.0362-0.0447-0.00990.0504-0.00240.2334-0.0043-0.03080.1809-0.04260.088930.8753-43.763591.9628
42.9715-0.2448-0.97423.2750.4443.0182-0.04360.2869-0.0732-0.25180.02550.2716-0.1834-0.2322-0.00780.23160.0159-0.07560.2094-0.00450.215717.1738-41.063291.0967
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 51 through 130 )
2X-RAY DIFFRACTION2chain 'A' and (resid 131 through 217 )
3X-RAY DIFFRACTION3chain 'B' and (resid 50 through 95 )
4X-RAY DIFFRACTION4chain 'B' and (resid 96 through 217 )

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