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- PDB-3m8j: Crystal structure of E.coli FocB at 1.4 A resolution -

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Basic information

Entry
Database: PDB / ID: 3m8j
TitleCrystal structure of E.coli FocB at 1.4 A resolution
ComponentsFocB protein
KeywordsTRANSCRIPTION / All-alpha / helix-turn-helix
Function / homologyAdhesin operon regulatory protein / Adhesin biosynthesis transcription regulatory protein / Arc Repressor Mutant, subunit A - #2690 / : / Arc Repressor Mutant, subunit A / regulation of DNA-templated transcription / Orthogonal Bundle / Mainly Alpha / FocB protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsHultdin, U.W. / Huang, S. / Sauer-Eriksson, A.E.
Citation
Journal: Febs J. / Year: 2010
Title: Structure of FocB - a member of a family of transcription factors regulating fimbrial adhesin expression in uropathogenic Escherichia coli
Authors: Hultdin, U.W. / Lindberg, S. / Grundstrom, C. / Huang, S. / Uhlin, B.E. / Sauer-Eriksson, A.E.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Purification, crystallization and preliminary data analysis of FocB, a transcription factor regulating fimbrial adhesin expression in uropathogenic Escherichia coli
Authors: Hultdin, U.W. / Lindberg, S. / Grundstrom, C. / Allgardsson, A. / Huang, S. / Stier, G. / Ohman, A. / Uhlin, B.E. / Sauer-Eriksson, A.E.
History
DepositionMar 18, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FocB protein
B: FocB protein


Theoretical massNumber of molelcules
Total (without water)24,3522
Polymers24,3522
Non-polymers00
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-15 kcal/mol
Surface area9840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.390, 58.823, 65.840
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 FocB protein / Putative F1C and S fimbrial switch regulatory protein SfaB / Putative uncharacterized protein / ...Putative F1C and S fimbrial switch regulatory protein SfaB / Putative uncharacterized protein / SfaB / SfaB protein


Mass: 12175.901 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: J96 / Gene: focB, sfaB / Plasmid: pET-M11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 pLysS / References: UniProt: Q93K76
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 1.88 Å3/Da / Density % sol: 34.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.5M magnesium sulphate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9792, 0.97945, 0.97535
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 6, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.979451
30.975351
ReflectionResolution: 1.4→50 Å / Num. obs: 36163 / % possible obs: 97.8 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 28.6
Reflection shellResolution: 1.4→1.47 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 6.1 / % possible all: 97.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
Auto-Rickshawphasing
REFMAC5.5.0072refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.4→18.79 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.994 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2216 1805 5 %RANDOM
Rwork0.19616 ---
obs0.19745 34198 97.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.007 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.4→18.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1396 0 0 148 1544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221418
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6111.9771905
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9585176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74622.45961
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74515258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8281512
X-RAY DIFFRACTIONr_chiral_restr0.1120.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021040
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2251.5876
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.16821398
X-RAY DIFFRACTIONr_scbond_it3.343542
X-RAY DIFFRACTIONr_scangle_it5.1214.5507
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 160 -
Rwork0.206 2449 -
obs--97.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7575-0.24050.45070.6302-0.46390.52260.03550.0895-0.0027-0.0363-0.0355-0.00070.01770.082400.01440.0096-0.00320.0406-0.01010.01727.515343.96637.6152
20.2591-0.1515-0.33480.47770.02480.6868-0.01280.00130.03470.0570.0350.01240.026-0.0119-0.02220.01810.00920.00060.02850.00190.03592.584734.390329.0212
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 99
2X-RAY DIFFRACTION2B10 - 97

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