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- PDB-2inw: Crystal structure of Q83JN9 from Shigella flexneri at high resolu... -

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Basic information

Entry
Database: PDB / ID: 2inw
TitleCrystal structure of Q83JN9 from Shigella flexneri at high resolution. Northeast Structural Genomics Consortium target SfR137.
ComponentsPutative structural protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Q83JN9 X-Ray NESG SfR137 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


positive regulation of cytoskeleton organization
Similarity search - Function
Antitoxin CbeA / Antitoxin CbeA superfamily / CbeA_antitoxin, type IV, cytoskeleton bundling-enhancing factor A / PAS domain / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Structural protein / Putative structural protein
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsKuzin, A.P. / Su, M. / Jayaraman, S. / Vorobiev, S.M. / Wang, D. / Jiang, M. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. ...Kuzin, A.P. / Su, M. / Jayaraman, S. / Vorobiev, S.M. / Wang, D. / Jiang, M. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Structure / Year: 2010
Title: Crystal Structures of Phd-Doc, HigA, and YeeU Establish Multiple Evolutionary Links between Microbial Growth-Regulating Toxin-Antitoxin Systems.
Authors: Arbing, M.A. / Handelman, S.K. / Kuzin, A.P. / Verdon, G. / Wang, C. / Su, M. / Rothenbacher, F.P. / Abashidze, M. / Liu, M. / Hurley, J.M. / Xiao, R. / Acton, T. / Inouye, M. / Montelione, ...Authors: Arbing, M.A. / Handelman, S.K. / Kuzin, A.P. / Verdon, G. / Wang, C. / Su, M. / Rothenbacher, F.P. / Abashidze, M. / Liu, M. / Hurley, J.M. / Xiao, R. / Acton, T. / Inouye, M. / Montelione, G.T. / Woychik, N.A. / Hunt, J.F.
History
DepositionOct 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 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

Downloads & links

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Assembly

Deposited unit
A: Putative structural protein
B: Putative structural protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0083
Polymers29,9132
Non-polymers951
Water4,540252
1
A: Putative structural protein


Theoretical massNumber of molelcules
Total (without water)14,9561
Polymers14,9561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative structural protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0512
Polymers14,9561
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.499, 73.967, 110.698
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative structural protein


Mass: 14956.386 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: yeeU, SF2998, S_3203 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL(21) + Magic / References: UniProt: Q83JN9, UniProt: A0A0H2VX33*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.15 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M Kh2PO4, 0.1M MES, 20% PEG20K, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 26, 2006 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. all: 77681 / Num. obs: 41154 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 24.9
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2 / % possible all: 79.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQUANTUMdata collection
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→19.42 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 144000.44 / 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
Rfree0.25 3319 4.9 %RANDOM
Rwork0.225 ---
obs0.225 39905 84.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.2607 Å2 / ksol: 0.325375 e/Å3
Displacement parametersBiso mean: 20.2 Å2
Baniso -1Baniso -2Baniso -3
1-5.61 Å20 Å20 Å2
2---2.15 Å20 Å2
3----3.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.5→19.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1813 0 5 252 2070
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.319 369 5.4 %
Rwork0.297 6485 -
obs--51.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.param

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