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- PDB-5m27: Structure of a bacterial light-regulated adenylyl cylcase -

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Basic information

Entry
Database: PDB / ID: 5m27
TitleStructure of a bacterial light-regulated adenylyl cylcase
ComponentsBeta subunit of photoactivated adenylyl cyclase
KeywordsLYASE / BLUF / adenylyl cyclase / photoreceptor / optogenetics
Function / homology
Function and homology information


cyclic nucleotide biosynthetic process / blue light photoreceptor activity / adenylate cyclase activity / FAD binding / cell projection / intracellular signal transduction / ATP binding / metal ion binding
Similarity search - Function
Sensors of blue-light using FAD / BLUF domain profile. / BLUF domain / Sensors of blue-light using FAD / Acylphosphatase-like domain superfamily / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Nucleotide cyclase
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Beta subunit of photoactivated adenylyl cyclase
Similarity search - Component
Biological speciesBeggiatoa sp. PS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLindner, R. / Hartmann, E. / Tarnawski, M. / Winkler, A. / Frey, D. / Reinstein, J. / Meinhart, A. / Schlichting, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationFOR1279 Germany
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Photoactivation Mechanism of a Bacterial Light-Regulated Adenylyl Cyclase.
Authors: Lindner, R. / Hartmann, E. / Tarnawski, M. / Winkler, A. / Frey, D. / Reinstein, J. / Meinhart, A. / Schlichting, I.
History
DepositionOct 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Jan 17, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_audit_support / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _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: Beta subunit of photoactivated adenylyl cyclase
B: Beta subunit of photoactivated adenylyl cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,45812
Polymers80,2532
Non-polymers1,20610
Water6,557364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9360 Å2
ΔGint-162 kcal/mol
Surface area29410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.330, 56.570, 78.110
Angle α, β, γ (deg.)104.280, 104.240, 102.180
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Beta subunit of photoactivated adenylyl cyclase


Mass: 40126.441 Da / Num. of mol.: 2 / Fragment: Beggiatoa photoactivatable adenylyl cyclase bPAC
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Beggiatoa sp. PS (bacteria) / Gene: BGP_1043 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A7BT71
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 0.1 M Na-MES pH 6.5, 0.2 M CaCl2,0.6 M NaCl, 20 % w/v PEG 3350; 3% w/v 1,6-diaminohexane in drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2010
RadiationMonochromator: DOUBLE-CRYSTAL Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2→44.915 Å / Num. obs: 48658 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 27.21 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.058 / Χ2: 0.981 / Net I/σ(I): 18.34 / Num. measured all: 170587
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2-2.10.3434.3823781687665870.8820.40495.8
2.1-2.20.2336.1719040562254340.9320.27696.7
2.2-2.40.1588.7229411867983820.9660.18896.6
2.4-2.60.10612.4521641622360470.9840.12597.2
2.6-2.80.07515.3714907456244330.9880.09197.2
2.8-30.05521.1812158347333680.9940.06597
3-40.03331.6828777860383220.9970.03996.7
4-60.02444.9814620444742780.9970.02996.2
6-100.02545.674851145014110.9970.03197.3
10-44.9150.02254.2314014053960.9970.02697.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BYC and 1WC0

2byc

1wc0


Resolution: 2→44.915 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 24.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2427 1453 2.99 %
Rwork0.2108 47204 -
obs0.2117 48657 96.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.32 Å2 / Biso mean: 33.7508 Å2 / Biso min: 11.57 Å2
Refinement stepCycle: final / Resolution: 2→44.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5413 0 70 364 5847
Biso mean--52.13 35.86 -
Num. residues----678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085600
X-RAY DIFFRACTIONf_angle_d0.9027594
X-RAY DIFFRACTIONf_chiral_restr0.056904
X-RAY DIFFRACTIONf_plane_restr0.006940
X-RAY DIFFRACTIONf_dihedral_angle_d18.5112096
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.07150.29111450.25474649479496
2.0715-2.15450.27431450.24654716486197
2.1545-2.25250.28861440.23464669481396
2.2525-2.37130.24391470.2324762490997
2.3713-2.51980.25151460.22924724487097
2.5198-2.71440.28421470.22414761490897
2.7144-2.98750.2621470.23314754490197
2.9875-3.41960.25171430.21024708485197
3.4196-4.30780.23461450.18724734487997
4.3078-44.92660.19821440.18774727487197
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)
10.0068-0.0106-0.02790.00650.02010.0879-0.22030.113-0.14440.1636-0.2371-0.14980.539-0.3344-00.3365-0.0044-0.01350.2932-0.04010.2352-23.3362-19.7812-33.3049
2-0.08560.05910.11530.30640.32020.56760.05080.0998-0.02370.1289-0.0582-0.09410.1748-0.029700.320.0073-0.02530.2578-0.02820.1435-21.2686-20.0992-37.9577
30.7853-0.0466-0.00020.6786-0.2929-0.02480.034-0.0562-0.0529-0.0314-0.02240.0223-0.0175-0.0022-00.0935-0.0034-0.00870.1026-0.02630.0967-16.7876-17.4997-0.229
4-0.01890.31460.01520.29830.30660.8120.06090.0279-0.1091-0.0363-0.00380.1357-0.14160.15300.30250.01530.01870.29160.03840.1218-10.54743.4194-38.4364
50.3413-0.35770.05930.64240.1328-0.06310.0251-0.02460.027-0.0309-0.01150.0057-0.02150.024800.1246-0.01290.01330.11950.0290.1347-16.48844.2612-4.0774
60.09980.10970.19480.13860.54830.311-0.1802-0.37230.32670.2102-0.0207-0.28850.0106-0.013-00.09790.01990.01010.1507-0.03650.0963-15.884711.256311.3429
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 13 )A2 - 13
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 126 )A16 - 126
3X-RAY DIFFRACTION3chain 'A' and (resid 127 through 347 )A127 - 347
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 126 )B1 - 126
5X-RAY DIFFRACTION5chain 'B' and (resid 127 through 285 )B127 - 285
6X-RAY DIFFRACTION6chain 'B' and (resid 286 through 347 )B286 - 347

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