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- PDB-3kcn: The crystal structure of adenylate cyclase from Rhodopirellula baltica -

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Basic information

Entry
Database: PDB / ID: 3kcn
TitleThe crystal structure of adenylate cyclase from Rhodopirellula baltica
ComponentsAdenylate cyclase homolog
KeywordsLYASE / SGX / adenylate cyclase / PSI 2 / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


phosphorelay response regulator activity / DNA-binding transcription activator activity / protein-DNA complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity / cytosol
Similarity search - Function
Transcriptional regulatory protein WalR-like / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Adenylate cyclase homolog
Similarity search - Component
Biological speciesRhodopirellula baltica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsZhang, Z. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: The crystal structure of adenylate cyclase from Rhodopirellula baltica
Authors: Zhang, Z. / Burley, S.K. / Swaminathan, S.
History
DepositionOct 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenylate cyclase homolog
B: Adenylate cyclase homolog


Theoretical massNumber of molelcules
Total (without water)34,5652
Polymers34,5652
Non-polymers00
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-8 kcal/mol
Surface area14030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.930, 103.096, 33.867
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Adenylate cyclase homolog


Mass: 17282.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopirellula baltica (bacteria) / Strain: Complete proteome / Gene: cyaA, RB11090 / Plasmid: BC-pSGX3 (BC) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)-codon +RIL -stratagene / References: UniProt: Q7UJS6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.14 Å3/Da / Density % sol: 42.65 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M HEPES sodium pH 7.5, 1.4 M sodium citrate tribasic dihydrate, VAPOR DIFFUSION, SITTING DROP, temperature 110K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 14, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.45→103.1 Å / Num. all: 11560 / Num. obs: 11538 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.3 % / Biso Wilson estimate: 28.9 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 15
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 9.4 / Num. unique all: 1652 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JK1

2jk1


Resolution: 2.45→65.552 Å / SU ML: 0.36 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.04 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2668 540 4.75 %RANDOM
Rwork0.2173 ---
obs0.2198 11379 98.68 %-
all-11379 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.522 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso mean: 17.54 Å2
Baniso -1Baniso -2Baniso -3
1-6.996 Å20 Å2-0 Å2
2---0.7672 Å20 Å2
3----6.2288 Å2
Refinement stepCycle: LAST / Resolution: 2.45→65.552 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2118 0 0 126 2244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142132
X-RAY DIFFRACTIONf_angle_d1.4982875
X-RAY DIFFRACTIONf_dihedral_angle_d19.176810
X-RAY DIFFRACTIONf_chiral_restr0.095343
X-RAY DIFFRACTIONf_plane_restr0.005369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.69650.30161310.21582601X-RAY DIFFRACTION98
2.6965-3.08670.261410.21832671X-RAY DIFFRACTION99
3.0867-3.88890.28091430.19492702X-RAY DIFFRACTION99
3.8889-65.5750.23451250.22022865X-RAY DIFFRACTION99

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