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- PDB-2aca: X-ray structure of a putative adenylate cyclase Q87NV8 from Vibri... -

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Basic information

Entry
Database: PDB / ID: 2aca
TitleX-ray structure of a putative adenylate cyclase Q87NV8 from Vibrio parahaemolyticus at the 2.25 A resolution. Northeast Structural Genomics Target VpR19.
Componentsputative adenylate cyclaseAdenylyl cyclase
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NESG / VPR19 / Q87NV8 / adenylate cyclase / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


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
PHOSPHATE ION / Putative adenylate cyclase
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsKuzin, A.P. / Abashidze, M. / Vorobiev, S.M. / Forouhar, F. / Chen, Y. / Acton, T. / Xiao, R. / Conover, K. / Ma, L.-C. / Cunningham, K.E. ...Kuzin, A.P. / Abashidze, M. / Vorobiev, S.M. / Forouhar, F. / Chen, Y. / Acton, T. / Xiao, R. / Conover, K. / Ma, L.-C. / Cunningham, K.E. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
History
DepositionJul 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative adenylate cyclase
B: putative adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4047
Polymers44,9292
Non-polymers4755
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-50 kcal/mol
Surface area17290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.866, 41.964, 91.740
Angle α, β, γ (deg.)90.00, 125.66, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein putative adenylate cyclase / Adenylyl cyclase


Mass: 22464.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Gene: VP1760 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q87NV8
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 18% PEG3350, 0.2M Ammonium Phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. all: 37820 / Num. obs: 37420 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 26.5 Å2 / Rsym value: 0.046

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.25→19.86 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 261272.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1694 5 %RANDOM
Rwork0.227 ---
obs-33948 95.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.1397 Å2 / ksol: 0.346042 e/Å3
Displacement parametersBiso mean: 33.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å23.25 Å2
2--4.95 Å20 Å2
3----4.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.25→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2860 0 25 150 3035
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.64
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.296 270 4.9 %
Rwork0.229 5230 -
obs--92.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4peg.parpeg.top

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