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- PDB-6yii: Crystal structure of a Class III adenylyl cyclase-like ATP-bindin... -

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Basic information

Entry
Database: PDB / ID: 6yii
TitleCrystal structure of a Class III adenylyl cyclase-like ATP-binding protein from Pseudomonas aeruginosa
ComponentsTranscriptional regulator
KeywordsSIGNALING PROTEIN / ATP Complex / Class III adenylyl cyclase fold
Function / homology
Function and homology information


cyclic nucleotide biosynthetic process / adenylate cyclase activity / intracellular signal transduction
Similarity search - Function
Nucleotide cyclase, GGDEF 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 / : / Adenylate and Guanylate cyclase catalytic domain protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.44 Å
AuthorsMoniot, S. / Steegborn, C.
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Crystal structure of a class III adenylyl cyclase-like ATP-binding protein from Pseudomonas aeruginosa.
Authors: Linder, J. / Hupfeld, E. / Weyand, M. / Steegborn, C. / Moniot, S.
History
DepositionApr 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_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: Transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,64611
Polymers56,6621
Non-polymers98410
Water11,566642
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-113 kcal/mol
Surface area18590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.400, 74.680, 149.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Transcriptional regulator


Mass: 56662.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: CAZ10_26895, DZ962_04370, IPC1509_03400, IPC170_13765, IPC669_21205
Plasmid: pQE30 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Tuner pREP GroESL / References: UniProt: A6N5T2

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Non-polymers , 7 types, 652 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 642 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.08 Å3/Da / Density % sol: 60.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 22.5 % MPD, 75 mM Na acetate pH 4.8 and 15 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.44→30.54 Å / Num. obs: 126837 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 21.4 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.018 / Rrim(I) all: 0.0495 / Net I/σ(I): 20.7
Reflection shellResolution: 1.44→1.49 Å / Rmerge(I) obs: 1.066 / Num. unique obs: 12534 / CC1/2: 0.521 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIXdev 2666refinement
XDSdata reduction
Aimlessdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.44→30.54 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1473 --
Rwork0.1312 --
obs-126829 99.9 %
Displacement parametersBiso mean: 29.82 Å2
Refinement stepCycle: LAST / Resolution: 1.44→30.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3664 0 52 642 4358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00884108
X-RAY DIFFRACTIONf_angle_d1.01115608
X-RAY DIFFRACTIONf_chiral_restr0.075619
X-RAY DIFFRACTIONf_plane_restr0.0072756
X-RAY DIFFRACTIONf_dihedral_angle_d20.65421586

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