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- PDB-2fsq: Crystal Structure of the Conserved Protein of Unknown Function AT... -

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Basic information

Entry
Database: PDB / ID: 2fsq
TitleCrystal Structure of the Conserved Protein of Unknown Function ATU0111 from Agrobacterium tumefaciens str. C58
ComponentsAtu0111 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta barrel / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Phosphoesterase SP1827 / 2H-phosphodiesterase-like, Domain of unknown function DUF1868 / Domain of unknown function (DUF1868) / Cyclic Phosphodiesterase; Chain: A, / Cyclic phosphodiesterase / Cyclic phosphodiesterase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / DUF1868 domain-containing protein / :
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsKim, Y. / Joachimiak, A. / Xu, X. / Zheng, H. / Edwards, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of the Conserved Hypothetical Protein Atu0111 from Agrobacterium tumefaciens str. C58
Authors: Kim, Y. / Joachimiak, A. / Xu, X. / Zheng, H. / Edwards, A. / Savchenko, A.
History
DepositionJan 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Atu0111 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3233
Polymers28,2031
Non-polymers1202
Water6,035335
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.926, 35.603, 51.189
Angle α, β, γ (deg.)89.70, 79.12, 69.44
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Atu0111 protein


Mass: 28202.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58 / Gene: atu0111 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q8UJ27, UniProt: A9CKP4*PLUS
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 38.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-tris, 0.2M Na(OAC), 30% PEG8K, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97912
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 20, 2005 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR, S1(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 1.4→21.88 Å / Num. obs: 39939 / % possible obs: 92.6 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 18
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 6.5 / % possible all: 75.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
MLPHAREphasing
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→21.88 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.271 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.077
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.20032 3961 9.9 %RANDOM
Rwork0.15376 ---
obs0.15843 35978 92.51 %-
all-35978 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.048 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.22 Å2-1.41 Å2
2---0.74 Å20.48 Å2
3---0.91 Å2
Refinement stepCycle: LAST / Resolution: 1.4→21.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1873 0 8 335 2216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222147
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.9562947
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3875272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.45722.991107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65115352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9031520
X-RAY DIFFRACTIONr_chiral_restr0.0820.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021744
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2410.21068
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21535
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2289
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.244
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1131.51332
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6522150
X-RAY DIFFRACTIONr_scbond_it2.6763912
X-RAY DIFFRACTIONr_scangle_it3.7144.5797
X-RAY DIFFRACTIONr_rigid_bond_restr1.9232147
X-RAY DIFFRACTIONr_sphericity_free20.2543335
X-RAY DIFFRACTIONr_sphericity_bonded5.93332073
LS refinement shellResolution: 1.401→1.438 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 191 -
Rwork0.182 2082 -
obs--72.04 %

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