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- PDB-3n10: Product complex of adenylate cyclase class IV -

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Basic information

Entry
Database: PDB / ID: 3n10
TitleProduct complex of adenylate cyclase class IV
ComponentsAdenylate cyclase 2Adenylyl cyclase
KeywordsLYASE / CYTH DOMAIN / ANTIPARALLEL BARREL / PRODUCT COMPLEX / CYCLIC AMP
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
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / : / Adenylate cyclase 2 / Adenylate cyclase 2
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsGallagher, D.T. / Reddy, P.T.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Active-Site Structure of Class IV Adenylyl Cyclase and Transphyletic Mechanism.
Authors: Gallagher, D.T. / Kim, S.K. / Robinson, H. / Reddy, P.T.
History
DepositionMay 14, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionJun 23, 2010ID: 3GHX
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 22, 2017Group: Source and taxonomy
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 6, 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenylate cyclase 2
B: Adenylate cyclase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7249
Polymers40,7082
Non-polymers1,0157
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-77 kcal/mol
Surface area16250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.477, 38.124, 80.658
Angle α, β, γ (deg.)90.000, 98.710, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Adenylate cyclase 2 / Adenylyl cyclase / Putative adenylate cyclase


Mass: 20354.143 Da / Num. of mol.: 2 / Mutation: D55K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: cyaB, y3011, YPO1178, YP_0959 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q7CH76, UniProt: A0A5P8YEL9*PLUS, adenylate cyclase
#2: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP / Cyclic adenosine monophosphate


Mass: 329.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O6P
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.41 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 45 MG/ML PTN, 7% PEG 5K MME, 0.1M AMS, 0.1M MES, PH 5.6, MACROSEEDING TO GROW BIG SINGLES, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 11, 2008
RadiationMonochromator: coated mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 49467 / Num. obs: 49467 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.06 / Χ2: 1.939 / Net I/σ(I): 14.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.6620.43132410.502162.9
1.66-1.723.90.39448200.573194.3
1.72-1.86.20.31951250.727199.7
1.8-1.97.20.23251250.9631100
1.9-2.027.30.16151981.361100
2.02-2.177.20.11851131.816199.9
2.17-2.397.20.09252012.252199.9
2.39-2.747.20.07551622.61100
2.74-3.4570.05352462.9861100
3.45-306.80.04652363.462197.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.3 Å9.99 Å
Translation3.3 Å9.99 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.2phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FJT

2fjt


Resolution: 1.6→16 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.251 / WRfactor Rwork: 0.218 / Occupancy max: 1 / Occupancy min: 0.8 / FOM work R set: 0.821 / SU B: 1.945 / SU ML: 0.07 / SU R Cruickshank DPI: 0.106 / SU Rfree: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2516 5.1 %RANDOM
Rwork0.218 ---
all0.219 ---
obs0.219 49428 95.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.37 Å2 / Biso mean: 28.332 Å2 / Biso min: 15.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å2-0.22 Å2
2---0.18 Å20 Å2
3---0.02 Å2
Refine analyzeLuzzati coordinate error free: 0.105 Å
Refinement stepCycle: LAST / Resolution: 1.6→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2812 0 57 171 3040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222922
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8041.9753954
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9165350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47924.722144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.58415516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9671516
X-RAY DIFFRACTIONr_chiral_restr0.1380.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022190
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.21189
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21926
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2151
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.481.51804
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.09822808
X-RAY DIFFRACTIONr_scbond_it3.24931266
X-RAY DIFFRACTIONr_scangle_it4.7364.51146
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 100 -
Rwork0.302 1937 -
all-2037 -
obs--53.89 %

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