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- PDB-3ssx: E. coli trp aporeporessor L75F mutant -

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Basic information

Entry
Database: PDB / ID: 3ssx
TitleE. coli trp aporeporessor L75F mutant
ComponentsTrp operon repressor
KeywordsDNA BINDING PROTEIN / Helix-turn-Helix motif / DNA binding / trp operator
Function / homology
Function and homology information


sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
TrpR-like / Trp repressor, bacterial / Trp repressor / TrpR-like superfamily / Trp repressor protein / Trp repressor/replication initiator / Trp Operon Repressor; Chain A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Trp operon repressor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5801 Å
AuthorsBenoff, B. / Carey, J. / Berman, H.M. / Lawson, C.L.
CitationJournal: Protein Sci. / Year: 2012
Title: Environment-dependent long-range structural distortion in a temperature-sensitive point mutant.
Authors: Carey, J. / Benoff, B. / Harish, B. / Yuan, L. / Lawson, C.L.
History
DepositionJul 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2011Group: Database references
Revision 1.2Dec 28, 2011Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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
R: Trp operon repressor
N: Trp operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7093
Polymers24,5462
Non-polymers1631
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-34 kcal/mol
Surface area11310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.716, 54.105, 55.633
Angle α, β, γ (deg.)90.000, 100.100, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Trp operon repressor


Mass: 12272.950 Da / Num. of mol.: 2 / Mutation: L75F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b4393, JW4356, rtrY, trpR / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A881
#2: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.16 Å3/Da / Density % sol: 42.95 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Hampton Research Crystal Screen condition #6: 30% (w/v) PEG 4000, 200 mM MgCl2, 100 mM Tris HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 21, 2002
RadiationMonochromator: channel-cut Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. all: 28206 / Num. obs: 28206 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.68 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.073 / Χ2: 2.624 / Net I/σ(I): 12.1
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.58-1.640.4961.9425091.133187.7
1.64-1.70.48427751.193196.3
1.7-1.780.39128331.256199.9
1.78-1.870.30528771.407199.9
1.87-1.990.228761.797199.9
1.99-2.140.13928552.41199.9
2.14-2.360.10428683.1061100
2.36-2.70.08428853.756199.9
2.7-3.40.06328984.262199.8
3.4-500.05228304.901196

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OZ9 DIMER

2oz9


Resolution: 1.5801→27.386 Å / Occupancy max: 1 / Occupancy min: 0.25 / SU ML: 0.02 / Cross valid method: maximum likelihood / σ(F): 1.35 / Phase error: 25.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2185 1323 4.99 %5% random selection
Rwork0.1755 ---
obs0.1776 26533 92.44 %-
all-26533 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 78.363 Å2 / ksol: 0.407 e/Å3
Displacement parametersBiso max: 112.64 Å2 / Biso mean: 36.3382 Å2 / Biso min: 16.85 Å2
Baniso -1Baniso -2Baniso -3
1--10.1326 Å20 Å2-6.9837 Å2
2---4.8388 Å2-0 Å2
3---14.9714 Å2
Refinement stepCycle: LAST / Resolution: 1.5801→27.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1623 0 11 238 1872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0241729
X-RAY DIFFRACTIONf_angle_d1.7882345
X-RAY DIFFRACTIONf_chiral_restr0.151261
X-RAY DIFFRACTIONf_plane_restr0.011307
X-RAY DIFFRACTIONf_dihedral_angle_d16.32698
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.5801-1.64340.28981010.248719102011201164
1.6434-1.71810.27751310.253224382569256981
1.7181-1.80870.28951310.223528562987298794
1.8087-1.9220.23791600.200129853145314599
1.922-2.07030.23321740.1686301031843184100
2.0703-2.27860.19531710.1608301231833183100
2.2786-2.60810.20431500.1664302831783178100
2.6081-3.28510.23471540.1666304732013201100
3.2851-27.38980.19761510.164529243075307594
Refinement TLS params.Method: refined / Origin x: 0.2543 Å / Origin y: 0.0476 Å / Origin z: 18.001 Å
111213212223313233
T0.183 Å2-0.0033 Å20.0063 Å2-0.1788 Å20.0015 Å2--0.182 Å2
L1.0407 °20.1108 °20.4056 °2-0.4898 °20.0858 °2--0.7006 °2
S-0.0166 Å °0.1473 Å °0.0532 Å °-0.0196 Å °0.008 Å °0.0555 Å °0.0154 Å °0.0343 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allR5 - 106
2X-RAY DIFFRACTION1allN8 - 106
3X-RAY DIFFRACTION1allN1 - 350
4X-RAY DIFFRACTION1allN1

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