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- PDB-2aeg: X-Ray Crystal Structure of Protein Atu5096 from Agrobacterium tum... -

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Basic information

Entry
Database: PDB / ID: 2aeg
TitleX-Ray Crystal Structure of Protein Atu5096 from Agrobacterium tumefaciens. Northeast Structural Genomics Consortium Target AtR63.
Componentshypothetical protein AGR_pAT_140
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein. / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


protein-DNA covalent cross-linking repair / Hydrolases; Acting on peptide bonds (peptidases) / peptidase activity / single-stranded DNA binding / lyase activity / proteolysis
Similarity search - Function
Thrombin, subunit H - #510 / hypothetical protein yedk fold - #20 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #570 / hypothetical protein yedk fold / SOS response associated peptidase (SRAP) / SOS response associated peptidase-like / SOS response associated peptidase (SRAP) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special ...Thrombin, subunit H - #510 / hypothetical protein yedk fold - #20 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #570 / hypothetical protein yedk fold / SOS response associated peptidase (SRAP) / SOS response associated peptidase-like / SOS response associated peptidase (SRAP) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Thrombin, subunit H / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Abasic site processing protein / :
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsForouhar, F. / Abashidze, M. / Kuzin, A.P. / Vorobiev, S.M. / Shastry, R. / Cooper, B. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the Hypothetical Protein Atu5096 from Agrobacterium tumefaciens.
Authors: Forouhar, F. / Abashidze, M. / Kuzin, A.P. / Vorobiev, S.M. / Shastry, R. / Cooper, B. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionJul 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 16, 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
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: hypothetical protein AGR_pAT_140
B: hypothetical protein AGR_pAT_140
C: hypothetical protein AGR_pAT_140


Theoretical massNumber of molelcules
Total (without water)93,0933
Polymers93,0933
Non-polymers00
Water6,323351
1
A: hypothetical protein AGR_pAT_140


Theoretical massNumber of molelcules
Total (without water)31,0311
Polymers31,0311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hypothetical protein AGR_pAT_140


Theoretical massNumber of molelcules
Total (without water)31,0311
Polymers31,0311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: hypothetical protein AGR_pAT_140


Theoretical massNumber of molelcules
Total (without water)31,0311
Polymers31,0311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)195.926, 73.994, 65.566
Angle α, β, γ (deg.)90.00, 106.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein hypothetical protein AGR_pAT_140


Mass: 31031.090 Da / Num. of mol.: 3 / Fragment: Atu5096
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58 / Gene: Atu5096 / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q8UKK6, UniProt: A9CLP4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.59 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM Bis-Tris (pH 5.5), 20% PEG 3350, 220 mM (NH)4 Acetate, and 5 mM DTT., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97913 / Wavelength: 0.97913 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 18, 2005 / Details: mirrors.
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97913 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 78562 / Num. obs: 77934 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.061 / Net I/σ(I): 15.61
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 4.85 / Num. unique all: 7829 / Rsym value: 0.229 / % possible all: 99.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→29.81 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 384490.25 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
Details: SnB was run prior to SOLVE/RESOLVE. XtalView was used in addition to CNS to refine the structure.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 7141 9.9 %RANDOM
Rwork0.217 ---
all0.219 77934 --
obs0.217 72406 92.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.3985 Å2 / ksol: 0.32095 e/Å3
Displacement parametersBiso mean: 30.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.63 Å20 Å2-8.23 Å2
2---2.34 Å20 Å2
3---5.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5865 0 0 351 6216
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.292 1029 9.9 %
Rwork0.249 9384 -
obs-9384 79.8 %

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