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- PDB-3mjq: Crystal structure of the PAS domain of Q24QT8_DESHY protein from ... -

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Basic information

Entry
Database: PDB / ID: 3mjq
TitleCrystal structure of the PAS domain of Q24QT8_DESHY protein from Desulfitobacterium hafniense. Northeast Structural Genomics Consortium Target DhR85c.
Componentsuncharacterized protein
Keywordsstructural genomics / unknown function / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


phosphorelay signal transduction system
Similarity search - Function
Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / PAS domain / Nucleotide cyclase / PAS domain / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain ...Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / PAS domain / Nucleotide cyclase / PAS domain / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Beta-Lactamase / PAS repeat profile. / PAS domain / PAS domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Stage 0 sporulation protein A homolog
Similarity search - Component
Biological speciesDesulfitobacterium hafniense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.601 Å
AuthorsVorobiev, S. / Neely, H. / Seetharaman, J. / Wang, D. / Ciccosanti, C. / Mao, L. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. ...Vorobiev, S. / Neely, H. / Seetharaman, J. / Wang, D. / Ciccosanti, C. / Mao, L. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the PAS domain of Q24QT8_DESHY protein from Desulfitobacterium hafniense.
Authors: Vorobiev, S. / Neely, H. / Seetharaman, J. / Wang, D. / Ciccosanti, C. / Mao, L. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionApr 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software
Revision 1.3Oct 6, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: uncharacterized protein
B: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)29,2782
Polymers29,2782
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-13 kcal/mol
Surface area11210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.609, 49.609, 190.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsDimer according to aggregation screening

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Components

#1: Protein uncharacterized protein


Mass: 14639.234 Da / Num. of mol.: 2 / Fragment: PAS domain / Mutation: P35T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfitobacterium hafniense (bacteria)
Strain: Y51 / Gene: DSY3815 / Plasmid: pET 21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) +Magic / References: UniProt: Q24QT8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.01 Å3/Da / Density % sol: 38.71 %
Crystal growTemperature: 291 K / Method: microbatch under paraffin oil / pH: 8.5
Details: 30% PEG 4000, 0.2M magnesium chloride, 0.1M Tris, pH 8.5, microbatch under paraffin oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 7832 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 19.9
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.676 / Mean I/σ(I) obs: 1.98 / Num. unique all: 2774 / % possible all: 96.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SnBphasing
PHENIX(phenix.refine: 1.6_289)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.601→34.402 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2783 360 4.6 %RANDOM
Rwork0.2372 ---
obs0.239 7832 98.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.356 Å2 / ksol: 0.348 e/Å3
Refinement stepCycle: LAST / Resolution: 2.601→34.402 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1670 0 0 18 1688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091702
X-RAY DIFFRACTIONf_angle_d1.5662290
X-RAY DIFFRACTIONf_dihedral_angle_d18.613644
X-RAY DIFFRACTIONf_chiral_restr0.097263
X-RAY DIFFRACTIONf_plane_restr0.006283
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6007-2.97680.41181080.34912411X-RAY DIFFRACTION99
2.9768-3.74980.28651170.23282478X-RAY DIFFRACTION99
3.7498-34.40480.24941350.21292583X-RAY DIFFRACTION97
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1refined2.24111.65980.0948-0.37161.15991.86680.00550.12090.04510.0006-0.2214-0.0411-0.2671-0.231300.4380.0326-0.05350.4507-0.03970.43557.984520.99561.1311
2-0.04760.2818-0.25950.74240.89451.6141-0.13060.1772-0.1806-0.01690.10480.069-0.37910.1825-00.4845-0.0678-0.06250.50770.00690.4072
Refinement TLS groupSelection details: chain B

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