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- PDB-2fjt: Adenylyl cyclase class iv from Yersinia pestis -

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Basic information

Entry
Database: PDB / ID: 2fjt
TitleAdenylyl cyclase class iv from Yersinia pestis
ComponentsAdenylyl cyclase class IV
KeywordsLYASE / CYCLASE / beta barrel / dimer
Function / homology
Function and homology information


adenylate cyclase / lyase activity / nucleotide binding / metal ion binding
Similarity search - Function
Adenylyl cyclase CyaB / Hypothetical Protein Pfu-838710-001 / Hypothetical Protein Pfu-838710-001 / CYTH / CYTH domain / CYTH domain / CYTH domain profile. / CYTH-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Adenylate cyclase 2 / Adenylate cyclase 2
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsGallagher, D.T. / Smith, N.N. / Kim, S.-K. / Reddy, P.T. / Robinson, H. / Heroux, A.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: Structure of the class IV adenylyl cyclase reveals a novel fold
Authors: Gallagher, D.T. / Smith, N.N. / Kim, S.-K. / Heroux, A. / Robinson, H. / Reddy, P.T.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Crystallization of the class IV adenylyl cyclase from Yersinia pestis
Authors: Smith, N.N. / Kim, S.-K. / Reddy, P.T. / Gallagher, D.T.
History
DepositionJan 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Apr 3, 2024Group: 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 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1 QUATERNARY STRUCTURE FOR THIS ENTRY: DIMER THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ... BIOMOLECULE: 1 QUATERNARY STRUCTURE FOR THIS ENTRY: DIMER THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS (1 BIOLOGICAL DIMER). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenylyl cyclase class IV
B: Adenylyl cyclase class IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4694
Polymers41,2772
Non-polymers1922
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-48 kcal/mol
Surface area16900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.529, 35.548, 71.985
Angle α, β, γ (deg.)88.89, 82.63, 65.47
Int Tables number1
Space group name H-MP1
Detailsthe biol. assembly is a homodimer equal to the asymmetric unit.

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Components

#1: Protein Adenylyl cyclase class IV / E.C.4.6.1.1 / COG1437: Adenylate cyclase / class 4


Mass: 20638.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Triclinic form, pH 4.6 / Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: KIM / Production host: Escherichia coli (E. coli)
References: UniProt: Q7CH76, UniProt: A0A5P8YEL9*PLUS, adenylate cyclase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 1.87 Å3/Da / Density % sol: 34.35 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100 mM Ammonium sulfate, 100 mM Sodium acetate, 14% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 20, 2004
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 21019 / Num. obs: 20986 / % possible obs: 89.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.04 % / Rmerge(I) obs: 0.026 / Net I/σ(I): 15.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.04 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 3.9 / % possible all: 83.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
CrystalClear(MSC/RIGAKU)data reduction
AMoREphasing
REFMAC5.2refinement
CrystalClear(MSC/RIGAKU)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: orthorhombic crystal form

Resolution: 1.901→9.98 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.679 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.286 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27293 1280 6.1 %RANDOM
Rwork0.21227 ---
all0.21608 19540 --
obs0.21608 19540 88.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.005 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20.23 Å2-0.29 Å2
2---0.14 Å20.08 Å2
3---0.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.901→9.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2804 0 10 304 3118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222862
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.9583864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4335351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.14624.861144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.87715506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1961516
X-RAY DIFFRACTIONr_chiral_restr0.1080.2429
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022167
X-RAY DIFFRACTIONr_nbd_refined0.2150.21218
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21836
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.2208
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.275
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2750.216
X-RAY DIFFRACTIONr_mcbond_it1.031.51819
X-RAY DIFFRACTIONr_mcangle_it1.53122809
X-RAY DIFFRACTIONr_scbond_it2.4531178
X-RAY DIFFRACTIONr_scangle_it3.7364.51055
LS refinement shellResolution: 1.901→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.456 88 -
Rwork0.347 1279 -
obs--80.41 %

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