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- PDB-2nys: X-ray Crystal Structure of Protein AGR_C_3712 from Agrobacterium ... -

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Basic information

Entry
Database: PDB / ID: 2nys
TitleX-ray Crystal Structure of Protein AGR_C_3712 from Agrobacterium tumefaciens. Northeast Structural Genomics Consortium Target AtR88.
ComponentsAGR_C_3712p
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / AGR_C_3712 / SspB / Stringent starvation protein B / NESG / AtR88 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologySspB-like / Stringent starvation protein B / SspB-like superfamily / Stringent starvation protein B / SH3 type barrels. / Roll / Mainly Beta / Uncharacterized protein
Function and homology information
Biological speciesAgrobacterium tumefaciens str. C58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsVorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Zhao, L. / Ma, L.C. / Cunningham, K. / Nwosu, C. / Xiao, R. / Acton, T.B. / Montelione, G.T. ...Vorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Zhao, L. / Ma, L.C. / Cunningham, K. / Nwosu, C. / Xiao, R. / 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_3712 from Agrobacterium tumefaciens.
Authors: Vorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Zhao, L. / Ma, L.C. / Cunningham, K. / Nwosu, C. / Acton, T.B. / Xiao, R. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionNov 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 20, 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
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AGR_C_3712p
B: AGR_C_3712p


Theoretical massNumber of molelcules
Total (without water)40,3642
Polymers40,3642
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-22 kcal/mol
Surface area12060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.550, 137.550, 57.113
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein AGR_C_3712p


Mass: 20182.125 Da / Num. of mol.: 2 / Mutation: E122K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. C58 (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58-ATCC 33970 / Gene: AGR_C3712 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q8U561
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 3.34 Å3/Da / Density % sol: 63.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 27% PEG 400, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97929, 0.97956, 0.96791
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 6, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979291
20.979561
30.967911
ReflectionResolution: 2.7→30 Å / Num. all: 28772 / Num. obs: 27602 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 47.4 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 24.86
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.76 / Num. unique all: 2516 / % possible all: 87.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SnBphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→24.79 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 117149.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 961 4 %RANDOM
Rwork0.242 ---
obs0.242 24328 84.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.3567 Å2 / ksol: 0.32596 e/Å3
Displacement parametersBiso mean: 57.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20 Å2
2--0.37 Å20 Å2
3----0.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 2.7→24.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1838 0 0 34 1872
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.404 127 4.5 %
Rwork0.357 2724 -
obs--59.3 %
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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