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- PDB-8jsz: Crystal structure of a uridylate cyclase from Anabaena sp. -

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Basic information

Entry
Database: PDB / ID: 8jsz
TitleCrystal structure of a uridylate cyclase from Anabaena sp.
Componentsuridylate cyclase
KeywordsTRANSFERASE / Adenylate/guanylate cyclase
Function / homologyACETATE ION
Function and homology information
Biological speciesAnabaena sp. CA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsWang, Y.-C. / Yang, C.-S. / Hou, M.-H. / Chen, Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)111-2311-B-039-001-MY3 Taiwan
CitationJournal: Nat Commun / Year: 2024
Title: Structural and functional characterization of cyclic pyrimidine-regulated anti-phage system.
Authors: Hou, M.H. / Chen, C.J. / Yang, C.S. / Wang, Y.C. / Chen, Y.
History
DepositionJun 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Database references / Structure summary / Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: uridylate cyclase
B: uridylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,61110
Polymers64,1072
Non-polymers5048
Water11,674648
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8910 Å2
ΔGint-68 kcal/mol
Surface area21080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.661, 50.792, 71.391
Angle α, β, γ (deg.)71.21, 83.96, 62.07
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein uridylate cyclase / adenylate/guanylate cyclase domain-containing protein


Mass: 32053.510 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: NCBI: WP_066377497.1 / Source: (gene. exp.) Anabaena sp. CA (bacteria) / Strain: ATCC 33047 / Gene: AnPycC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: uridylate cyclase

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Non-polymers , 5 types, 656 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 648 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.25 Å3/Da / Density % sol: 45.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BIS-TRIS pH 6.5, 0.2 M Magnesium chloride hexahydrate, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 07A / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.83→30 Å / Num. obs: 47377 / % possible obs: 97.6 % / Redundancy: 5.5 % / CC1/2: 0.998 / Net I/σ(I): 27.5
Reflection shellResolution: 1.84→1.91 Å / Redundancy: 5.3 % / Num. unique obs: 4637 / CC1/2: 0.972 / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.83→25.05 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.951 / Cross valid method: THROUGHOUT / ESU R: 0.374 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17893 22277 47.1 %RANDOM
Rwork0.17651 ---
obs0.17765 25040 96.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.504 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20.16 Å20.09 Å2
2---0.24 Å2-0.26 Å2
3---0.3 Å2
Refinement stepCycle: 1 / Resolution: 1.83→25.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4168 0 24 648 4840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0134282
X-RAY DIFFRACTIONr_bond_other_d0.0340.0174094
X-RAY DIFFRACTIONr_angle_refined_deg1.7311.6425786
X-RAY DIFFRACTIONr_angle_other_deg2.2251.5849412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1715512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.82923.578218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74415754
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6671518
X-RAY DIFFRACTIONr_chiral_restr0.0970.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024796
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021016
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.7491.8792068
X-RAY DIFFRACTIONr_mcbond_other4.6991.8742066
X-RAY DIFFRACTIONr_mcangle_it5.9862.7592572
X-RAY DIFFRACTIONr_mcangle_other5.9862.7632573
X-RAY DIFFRACTIONr_scbond_it6.3512.3052214
X-RAY DIFFRACTIONr_scbond_other6.3492.3072215
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.1013.2243215
X-RAY DIFFRACTIONr_long_range_B_refined8.96224.2325174
X-RAY DIFFRACTIONr_long_range_B_other8.98223.5415036
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.834→1.881 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 1356 -
Rwork0.211 1644 -
obs--82.78 %

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