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- PDB-3n0z: Adenylate cyclase class IV with active site ligand 3AT -

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Basic information

Entry
Database: PDB / ID: 3n0z
TitleAdenylate cyclase class IV with active site ligand 3AT
ComponentsAdenylate cyclase 2
KeywordsLYASE / CYTH domain / antiparallel barrel / substrate analog complex
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
3'-DEOXYADENOSINE-5'-TRIPHOSPHATE / : / Adenylate cyclase 2 / Adenylate cyclase 2
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 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
Revision 1.0Nov 24, 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_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.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_label_asym_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)41,8016
Polymers40,7082
Non-polymers1,0924
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-29 kcal/mol
Surface area16280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.543, 37.975, 81.277
Angle α, β, γ (deg.)90.000, 99.080, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Adenylate cyclase 2 / 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-3AT / 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE / CORDYCEPIN TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.42 Å3/Da / Density % sol: 49.09 %
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, 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: 1.7→30 Å / Num. all: 40701 / Num. obs: 40701 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.069 / Χ2: 0.831 / Net I/σ(I): 12.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.762.90.41128400.467166.2
1.76-1.834.80.36538820.548189.7
1.83-1.916.70.28941360.614196.1
1.91-2.027.50.18841460.739196.5
2.02-2.147.50.13242370.826197
2.14-2.317.50.10341560.899197.3
2.31-2.547.50.08542550.908197.7
2.54-2.917.40.06842620.9198.1
2.91-3.667.30.05943130.969198.5
3.66-3010.80.06544740.926199.2

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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
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FJT

2fjt


Resolution: 1.7→16 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.251 / WRfactor Rwork: 0.206 / Occupancy max: 1 / Occupancy min: 0.7 / FOM work R set: 0.814 / SU B: 2.54 / SU ML: 0.086 / SU R Cruickshank DPI: 0.124 / SU Rfree: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2031 5 %RANDOM
Rwork0.206 ---
obs0.208 40629 93.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.56 Å2 / Biso mean: 31.791 Å2 / Biso min: 18.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20 Å20.18 Å2
2---0.49 Å20 Å2
3----0.28 Å2
Refine analyzeLuzzati coordinate error free: 0.125 Å
Refinement stepCycle: LAST / Resolution: 1.7→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2802 0 62 198 3062
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222917
X-RAY DIFFRACTIONr_angle_refined_deg1.8231.983949
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4385349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.2824.755143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.05715515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5641516
X-RAY DIFFRACTIONr_chiral_restr0.1350.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022180
X-RAY DIFFRACTIONr_nbd_refined0.2190.21204
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21929
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2199
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.213
X-RAY DIFFRACTIONr_mcbond_it1.4281.51798
X-RAY DIFFRACTIONr_mcangle_it2.12722800
X-RAY DIFFRACTIONr_scbond_it3.31431270
X-RAY DIFFRACTIONr_scangle_it5.0564.51149
LS refinement shellResolution: 1.698→1.742 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 103 -
Rwork0.265 1852 -
all-1955 -
obs--61.3 %

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