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- PDB-1yk9: Crystal structure of a mutant form of the mycobacterial adenylyl ... -

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Basic information

Entry
Database: PDB / ID: 1yk9
TitleCrystal structure of a mutant form of the mycobacterial adenylyl cyclase Rv1625c
ComponentsAdenylate cyclaseAdenylyl cyclase
KeywordsLYASE / beta-alpha-beta sandwich / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


receptor guanylyl cyclase signaling pathway / peptide receptor activity / cGMP biosynthetic process / guanylate cyclase activity / adenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / manganese ion binding / membrane => GO:0016020 / intracellular signal transduction ...receptor guanylyl cyclase signaling pathway / peptide receptor activity / cGMP biosynthetic process / guanylate cyclase activity / adenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / manganese ion binding / membrane => GO:0016020 / intracellular signal transduction / magnesium ion binding / signal transduction / ATP binding / plasma membrane
Similarity search - Function
: / MASE7 / Nucleotide cyclase, GGDEF domain / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Nucleotide cyclase ...: / MASE7 / Nucleotide cyclase, GGDEF domain / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / 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
Adenylate cyclase / Adenylate cyclase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKetkar, A.D. / Shenoy, A.R. / Ramagopal, U.A. / Visweswariah, S.S. / Suguna, K. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Mol.Biol. / Year: 2006
Title: A Structural Basis for the Role of Nucleotide Specifying Residues in Regulating the Oligomerization of the Rv1625c Adenylyl Cyclase from M.tuberculosis
Authors: Ketkar, A.D. / Shenoy, A.R. / Ramagopal, U.A. / Visweswariah, S.S. / Suguna, K.
History
DepositionJan 17, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenylate cyclase


Theoretical massNumber of molelcules
Total (without water)22,3721
Polymers22,3721
Non-polymers00
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.020, 71.020, 43.739
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Adenylate cyclase / Adenylyl cyclase / ATP pyrophosphate-lyase / Adenylyl cyclase


Mass: 22372.295 Da / Num. of mol.: 1 / Fragment: Rv1625c catalytic domain / Mutation: K296E, F363R, D365C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv1625c / Plasmid: pRSET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: O30820, UniProt: P9WQ35*PLUS, adenylate cyclase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.66 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.9793 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 1, 2004
RadiationMonochromator: sagitally focusing Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.65→19.98 Å / Num. all: 6356 / Num. obs: 6355 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 9.5 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 11.8
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.8 / Num. unique all: 628 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→19.98 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 2007090.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 582 9.6 %RANDOM
Rwork0.205 ---
obs0.205 6079 99.3 %-
all-6345 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 300 Å2 / ksol: 1.16565 e/Å3
Displacement parametersBiso mean: 34.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2--0.13 Å20 Å2
3---0.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1410 0 0 71 1481
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_improper_angle_d1.16
X-RAY DIFFRACTIONc_mcbond_it4.81.5
X-RAY DIFFRACTIONc_mcangle_it7.442
X-RAY DIFFRACTIONc_scbond_it8.072
X-RAY DIFFRACTIONc_scangle_it9.782.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.388 98 9.7 %
Rwork0.236 912 -
obs-912 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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