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- PDB-3ssw: E. coli trp aporepressor -

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Basic information

Entry
Database: PDB / ID: 3ssw
TitleE. coli trp aporepressor
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: 1.6693 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
SupersessionAug 15, 2012ID: 1P6Z
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
R: Trp operon repressor
N: Trp operon repressor


Theoretical massNumber of molelcules
Total (without water)24,4782
Polymers24,4782
Non-polymers00
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-35 kcal/mol
Surface area11340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.692, 54.335, 56.945
Angle α, β, γ (deg.)90.000, 103.210, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Trp operon repressor


Mass: 12238.934 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.2 Å3/Da / Density % sol: 43.99 %
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: 1.669→50 Å / Num. all: 24536 / Num. obs: 24536 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 37.6 Å2 / Rmerge(I) obs: 0.066 / Χ2: 1.007 / Net I/σ(I): 13.2
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.669-1.730.5972.5223410.759194.8
1.73-1.80.44524710.809199.4
1.8-1.880.31124560.892199.3
1.88-1.980.20824311.082199.7
1.98-2.10.14824681.163199.8
2.1-2.270.10724631.3131100
2.27-2.490.08624841.3991100
2.49-2.860.0724831.21100
2.86-3.60.05824940.932199.8
3.6-500.04924450.389196.1

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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: 1.6693→24.045 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8482 / SU ML: 0.4 / Cross valid method: maximum likelihood / σ(F): 1 / Phase error: 22.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2194 2311 9.95 %10% random selection
Rwork0.1762 ---
obs0.1803 23235 93.84 %-
all-23235 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.935 Å2 / ksol: 0.415 e/Å3
Displacement parametersBiso max: 114.37 Å2 / Biso mean: 37.0888 Å2 / Biso min: 16.48 Å2
Baniso -1Baniso -2Baniso -3
1--5.4803 Å20 Å2-5.5099 Å2
2---2.3574 Å2-0 Å2
3---7.8377 Å2
Refinement stepCycle: LAST / Resolution: 1.6693→24.045 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1596 0 0 201 1797
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0221657
X-RAY DIFFRACTIONf_angle_d1.4912249
X-RAY DIFFRACTIONf_chiral_restr0.112258
X-RAY DIFFRACTIONf_plane_restr0.008295
X-RAY DIFFRACTIONf_dihedral_angle_d14.795649
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.6693-1.70340.27861230.23699951118111876
1.7034-1.74040.26211280.207110371165116583
1.7404-1.78090.22961210.185611601281128188
1.7809-1.82540.22511310.193311571288128889
1.8254-1.87470.23111430.178511981341134190
1.8747-1.92990.26241320.185811781310131093
1.9299-1.99210.25571380.174912781416141696
1.9921-2.06330.22991260.181812631389138997
2.0633-2.14580.20611490.164712571406140698
2.1458-2.24340.20181580.148913021460146099
2.2434-2.36160.22381520.167712691421142198
2.3616-2.50940.23071380.169412851423142399
2.5094-2.70290.23861520.176313161468146899
2.7029-2.97450.23181250.1816132214471447100
2.9745-3.40390.22721220.1691132514471447100
3.4039-4.28460.19251370.146113131450145098
4.2846-24.04770.19291360.18912691405140593
Refinement TLS params.Method: refined / Origin x: -0.7226 Å / Origin y: 0.1041 Å / Origin z: 17.9897 Å
111213212223313233
T0.1766 Å2-0.0025 Å2-0.0061 Å2-0.1491 Å20.0012 Å2--0.1618 Å2
L1.3753 °20.103 °2-0.0407 °2-0.5821 °2-0.0259 °2--0.9709 °2
S0.0232 Å °0.1373 Å °0.0341 Å °-0.0805 Å °-0.0168 Å °0.0593 Å °0.0731 Å °-0.0432 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allR5 - 105
2X-RAY DIFFRACTION1allN8 - 105
3X-RAY DIFFRACTION1allN1 - 336

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