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- PDB-2h28: Crystal structure of YeeU from E. coli. Northeast Structural Geno... -

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Basic information

Entry
Database: PDB / ID: 2h28
TitleCrystal structure of YeeU from E. coli. Northeast Structural Genomics target ER304
ComponentsHypothetical protein yeeU
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ER304 / E. coli / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


negative regulation of cell killing / positive regulation of cytoskeleton organization / cytoskeletal protein binding / metal ion binding / cytoplasm
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
Cytoskeleton bundling-enhancing antitoxin CbeA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsArbing, M. / Su, M. / Benach, J. / Karpowich, N.K. / Jiang, M. / Xiao, R. / Cunningham, K. / Ma, L.-C. / Chen, C.X. / Acton, T.B. ...Arbing, M. / Su, M. / Benach, J. / Karpowich, N.K. / Jiang, M. / Xiao, R. / Cunningham, K. / Ma, L.-C. / Chen, C.X. / Acton, T.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
DepositionMay 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 30, 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Hypothetical protein yeeU
B: Hypothetical protein yeeU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1837
Polymers29,9152
Non-polymers2685
Water1,47782
1
A: Hypothetical protein yeeU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0173
Polymers14,9571
Non-polymers602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Hypothetical protein yeeU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1664
Polymers14,9571
Non-polymers2083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-39 kcal/mol
Surface area11280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.216, 45.310, 60.185
Angle α, β, γ (deg.)90, 108.79, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hypothetical protein yeeU


Mass: 14957.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 MG1655 / Gene: yeeU / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: P76364
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.34 Å3/Da / Density % sol: 47.39 %
Crystal growTemperature: 293 K / Method: under oil / pH: 7
Details: MOPS, 0.1M MgSO4, 20% PEG 4000, pH 7.0, Under oil, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97901 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 15, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97901 Å / Relative weight: 1
ReflectionRedundancy: 2.2 % / Av σ(I) over netI: 12.3 / Number: 79229 / Rmerge(I) obs: 0.048 / Χ2: 1.38 / D res high: 2 Å / D res low: 100 Å / Num. obs: 35928 / % possible obs: 96.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.841008710.0291.6632.1
5.436.8498.410.0352.0272.2
4.745.4398.110.0342.2632.2
4.314.7497.110.0362.3342.2
44.3198.310.0392.3582.2
3.76497.910.0412.5422.2
3.583.7697.610.0412.3842.2
3.423.5896.410.0422.1492.2
3.293.4298.610.0472.2542.2
3.173.2998.210.0491.9872.2
3.083.1798.310.0491.8462.2
2.993.0898.710.0561.7582.2
2.912.9998.210.0561.5062.2
2.842.919910.061.442.2
2.772.8498.710.0641.3282.3
2.712.7798.410.0661.2762.2
2.662.7196.710.0771.2692.3
2.612.6698.910.0791.1582.3
2.562.6198.910.0811.0782.2
2.522.5698.510.0981.1342.3
2.482.5298.510.1071.0162.3
2.442.4899.210.1010.9792.2
2.412.4498.910.1220.9062.3
2.372.4198.510.1340.9712.3
2.342.3798.810.1380.8932.3
2.312.3499.110.1490.9762.3
2.282.3198.810.1630.9282.3
2.252.2894.810.2021.1572.3
2.232.259310.2261.1912.2
2.22.2398.510.2140.9542.3
2.182.298.910.2240.7872.2
2.152.1897.810.220.8712.3
2.132.1597.310.2850.92.3
2.112.1398.510.2940.8462.2
2.092.1198.110.350.8942.2
2.072.0994.710.4311.212.2
2.052.0790.510.4461.1652.1
2.032.0593.810.5370.971.9
2.022.0390.510.5470.8361.8
22.0287.310.5150.8581.8
ReflectionResolution: 2→100 Å / Num. all: 35928 / Num. obs: 35928 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Rmerge(I) obs: 0.048 / Χ2: 1.381 / Net I/σ(I): 12.3
Reflection shellResolution: 2→2.02 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.515 / Num. unique all: 836 / Χ2: 0.858 / % possible all: 87.3

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Phasing

PhasingMethod: SAD
Phasing dmFOM : 0.55 / FOM acentric: 0.55 / FOM centric: 0.61 / Reflection: 15362 / Reflection acentric: 14411 / Reflection centric: 951
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6-28.490.930.950.85694576118
3.8-60.930.940.8621681964204
3-3.80.840.840.827302545185
2.6-30.610.610.5326982553145
2.3-2.60.320.330.3144854285200
2.1-2.30.170.170.192587248899

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.08phasing
RESOLVE2.08phasing
CNSrefinement
PDB_EXTRACT2data extraction
ADSCdata collection
RefinementMethod to determine structure: SAD / Resolution: 2.1→40 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 746 4.6 %RANDOM
Rwork0.22 ---
all-16380 --
obs-15145 92.5 %-
Solvent computationBsol: 63.02 Å2
Displacement parametersBiso mean: 46.833 Å2
Baniso -1Baniso -2Baniso -3
1-7.45 Å20 Å2-0.482 Å2
2---7.671 Å20 Å2
3---0.221 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1689 0 15 82 1786
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.7541.5
X-RAY DIFFRACTIONc_scbond_it2.8582
X-RAY DIFFRACTIONc_mcangle_it2.9482
X-RAY DIFFRACTIONc_scangle_it4.4562.5
X-RAY DIFFRACTIONc_bond_d0.005567
X-RAY DIFFRACTIONc_angle_deg1.32477
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.par
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ligands_xplor_par.txt
X-RAY DIFFRACTION4ion.param

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