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- PDB-2oxl: Structure and Function of the E. coli Protein YmgB: a Protein Cri... -

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Basic information

Entry
Database: PDB / ID: 2oxl
TitleStructure and Function of the E. coli Protein YmgB: a Protein Critical for Biofilm Formation and Acid Resistance
ComponentsHypothetical protein ymgB
KeywordsGENE REGULATION / bacterial protein / biofilm / acid resistance / DNA binding protein / dimer
Function / homology
Function and homology information


single-species biofilm formation / cellular response to acidic pH / response to hydrogen peroxide / protein homodimerization activity / DNA binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #5260 / Regulatory protein AriR / Biofilm development protein YmgB/AriR / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Probable two-component-system connector protein AriR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsPage, R. / Peti, W. / Woods, T.K. / Palermino, J.M. / Doshi, O.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structure and Function of the Escherichia coli Protein YmgB: A Protein Critical for Biofilm Formation and Acid-resistance.
Authors: Lee, J. / Page, R. / Garcia-Contreras, R. / Palermino, J.M. / Zhang, X.S. / Doshi, O. / Wood, T.K. / Peti, W.
History
DepositionFeb 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein ymgB
B: Hypothetical protein ymgB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9244
Polymers14,3402
Non-polymers5852
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.919, 69.945, 55.021
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Hypothetical protein ymgB


Mass: 7169.856 Da / Num. of mol.: 2 / Fragment: YmgB C-terminal fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ymgB / Plasmid: RP-1B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: P75993
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.45 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 8
Details: 90 mM Tris, 1.8 M NaCl, 0.5 (w/v)% B-OG, pH 8.0, microbatch, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9790, 0.9793, 0.9322
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 25, 2006 / Details: Toroidal focusing mirror
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97931
30.93221
Reflection

D res high: 1.95 Å / D res low: 45 Å / % possible obs: 99.9

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2Num. obs
6.8127.1692450.0351.1410135
6.8227.5692590.0431.7810140
7.1325.1723220.0361.0910130
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.24599.410.0271.5766.6
3.334.210010.0251.1887.1
2.913.3310010.0321.1447.2
2.652.9110010.0381.0527.2
2.462.6510010.0431.1647.3
2.312.4610010.0541.1387.3
2.22.3110010.0681.0897.3
2.12.210010.0851.0737.3
2.022.110010.1130.9796.3
1.952.0299.610.1340.8634.7
4.24599.420.0373.536.6
3.334.210020.0332.2547.1
2.913.3310020.0412.0187.2
2.652.9110020.0461.6877.2
2.462.6510020.0511.7197.3
2.312.4610020.0611.5497.3
2.22.3110020.0731.3267.3
2.12.210020.0881.2337.3
2.022.110020.1161.1226.3
1.952.0299.620.141.0314.7
4.24599.530.0261.4436.6
3.334.210030.0251.0677.1
2.913.3310030.0321.0837.2
2.652.9110030.0381.0217.2
2.462.6510030.0461.1567.3
2.312.4610030.0561.1037.3
2.22.3110030.071.0397.3
2.12.210030.0871.0277.3
2.022.110030.1241.037.3
1.952.0210030.1620.9226.8
ReflectionResolution: 1.8→45 Å / Num. all: 12849 / Num. obs: 12802 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.6 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 22.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.403 / % possible all: 96.8

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.9795.83-7.65
13 wavelength20.97933.59-9.61
13 wavelength30.93223.43-2.9
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se40.7550.3360.210.2580.763
2Se37.6440.7910.3360.0080.744
Phasing dmFOM : 0.77 / FOM acentric: 0.77 / FOM centric: 0.74 / Reflection: 9402 / Reflection acentric: 8194 / Reflection centric: 1208
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.7-18.3880.960.970.96439302137
3.6-5.70.960.960.9612831053230
2.9-3.60.920.940.8615891369220
2.5-2.90.840.850.7515781401177
2.1-2.50.70.710.5927862500286
2-2.10.480.490.3317271569158

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.11phasing
RESOLVE2.11phasing
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.969 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23789 625 4.9 %RANDOM
Rwork0.21456 ---
obs0.21567 12174 99.67 %-
all-12849 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.249 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms954 0 40 31 1025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221012
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6662.0411374
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9925130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.362740
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.00915192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.786154
X-RAY DIFFRACTIONr_chiral_restr0.0870.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02680
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.2435
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.2732
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.233
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.267
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0570.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5393652
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.551022
X-RAY DIFFRACTIONr_scbond_it6.4638397
X-RAY DIFFRACTIONr_scangle_it9.08311348
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 45 -
Rwork0.313 855 -
obs--95.85 %
Refinement TLS params.Method: refined / Origin x: 9.85 Å / Origin y: -12.9414 Å / Origin z: -7.9944 Å
111213212223313233
T-0.0393 Å20.0312 Å20.0122 Å2-0.0305 Å20.0774 Å2--0.0054 Å2
L0.5248 °20.9578 °20.2063 °2-1.75 °20.3108 °2--2.5251 °2
S0.1139 Å °-0.0225 Å °0.0024 Å °-0.0206 Å °0.0435 Å °0.0644 Å °-0.1515 Å °-0.2382 Å °-0.1574 Å °

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