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- PDB-3db9: Crystal structure of UPF0317 protein Atu3911 from Agrobacterium t... -

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Basic information

Entry
Database: PDB / ID: 3db9
TitleCrystal structure of UPF0317 protein Atu3911 from Agrobacterium tumefaciens. NorthEast Strcutural Genomics target AtR186
ComponentsUPF0317 protein Atu3911
Keywordsstructural genomics / unknown function / Belongs to the UPF0317 family / Agrobacterium tumefaciens / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Lyases; Carbon-oxygen lyases; Hydro-lyases / lyase activity
Similarity search - Function
PSTPO5379-like fold / PSTPO5379-like domain / PSTPO5379-like / PSTPO5379-like / D-glutamate cyclase / Uncharacterised protein family UPF0317 / Putative hydro-lyase / D-glutamate cyclase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative hydro-lyase Atu3911
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. C58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSeetharaman, J. / Abashidze, M. / Wang, D. / Janjua, H. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. ...Seetharaman, J. / Abashidze, M. / Wang, D. / Janjua, H. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of UPF0317 protein Atu3911 from Agrobacterium tumefaciens. NorthEast Strcutural Genomics target AtR186 (CASP Target)
Authors: Seetharaman, J. / Abashidze, M. / Wang, D. / Janjua, H. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionMay 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPF0317 protein Atu3911


Theoretical massNumber of molelcules
Total (without water)28,9671
Polymers28,9671
Non-polymers00
Water2,306128
1
A: UPF0317 protein Atu3911

A: UPF0317 protein Atu3911


Theoretical massNumber of molelcules
Total (without water)57,9342
Polymers57,9342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area1290 Å2
ΔGint-8 kcal/mol
Surface area22210 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.374, 101.374, 84.325
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein UPF0317 protein Atu3911


Mass: 28967.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. C58 (bacteria)
Strain: Agrobacterium tumefaciens (strain C58 / ATCC 33970 / Gene: Atu3911, AGR_L_1868 / Plasmid: PET21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U919
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.16 Å3/Da / Density % sol: 43.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 200 mM NH4SO4, 20% PEG 4000, 50 mM MOPS pH 7. VAPOR DIFFUSION, SITTING 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 210 / Detector: CCD / Date: May 2, 2008 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 11899 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.8 % / Biso Wilson estimate: 105.8 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.062 / Net I/σ(I): 17.9
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 21 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 16 / Num. unique all: 1183 / Rsym value: 0.361 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PIF.pdb

2pif


Resolution: 2.8→38.94 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 226034.91 / 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
Rfree0.268 1096 10 %RANDOM
Rwork0.229 ---
obs0.229 11015 92.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.4671 Å2 / ksol: 0.368438 e/Å3
Displacement parametersBiso mean: 54.4 Å2
Baniso -1Baniso -2Baniso -3
1--12.84 Å22.45 Å20 Å2
2---10.97 Å20 Å2
3---23.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.8→38.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1758 0 0 128 1886
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_improper_angle_d1.17
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.492
X-RAY DIFFRACTIONc_scbond_it1.732
X-RAY DIFFRACTIONc_scangle_it2.732.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.399 168 10.3 %
Rwork0.278 1470 -
obs--82.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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