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- PDB-2axo: X-Ray Crystal Structure of Protein AGR_C_4864 from Agrobacterium ... -

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Basic information

Entry
Database: PDB / ID: 2axo
TitleX-Ray Crystal Structure of Protein AGR_C_4864 from Agrobacterium tumefaciens. Northeast Structural Genomics Consortium Target AtR35.
Componentshypothetical protein Atu2684
KeywordsUNKNOWN FUNCTION / alpha beta protein. / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyProtein of unknown function DUF1223 / Protein of unknown function (DUF1223) / Thioredoxin-like superfamily / DUF1223 domain-containing protein / :
Function and homology information
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsForouhar, F. / Abashidze, M. / Benach, J. / Xiao, R. / Janjua, H. / Conover, K. / 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 AGR_C_4864 from Agrobacterium tumefaciens, NESG target AtR35
Authors: Forouhar, F. / Abashidze, M. / Benach, J. / Xiao, R. / Janjua, H. / Conover, K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionSep 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 6, 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 Atu2684


Theoretical massNumber of molelcules
Total (without water)29,8231
Polymers29,8231
Non-polymers00
Water2,090116
1
A: hypothetical protein Atu2684

A: hypothetical protein Atu2684


Theoretical massNumber of molelcules
Total (without water)59,6462
Polymers59,6462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Unit cell
Length a, b, c (Å)44.017, 57.296, 143.895
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Detailspossibly dimer.

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Components

#1: Protein hypothetical protein Atu2684


Mass: 29822.830 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: MDK4.6 / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q8UC14, UniProt: A9CHH7*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 1.6 Å3/Da / Density % sol: 23.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20 mM Tris (pH 7.5), 18% PEG 2kMME, 200 mM sodium formate, 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: 0.97923 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 24, 2005 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.72→20 Å / Num. all: 37482 / Num. obs: 37295 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 10.5 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.064 / Net I/σ(I): 23.4
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1837 / Rsym value: 0.429 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 228678.5 / 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: XtalView and SnB were also used in the refinement and solution of this structure.
RfactorNum. reflection% reflectionSelection details
Rfree0.241 2850 9.6 %RANDOM
Rwork0.203 ---
all0.206 29592 --
obs0.203 29592 90.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.9 Å2 / ksol: 0.36423 e/Å3
Displacement parametersBiso mean: 19.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.7 Å20 Å20 Å2
2---0.8 Å20 Å2
3----2.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å-0.05 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1687 0 0 116 1803
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d0.71
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.262 394 9.7 %
Rwork0.195 3662 -
obs-3662 74.9 %

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