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- PDB-1tro: CRYSTAL STRUCTURE OF TRP REPRESSOR OPERATOR COMPLEX AT ATOMIC RES... -

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Basic information

Entry
Database: PDB / ID: 1tro
TitleCRYSTAL STRUCTURE OF TRP REPRESSOR OPERATOR COMPLEX AT ATOMIC RESOLUTION
Components
  • DNA (5'-D(*TP*GP*TP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*TP*AP*GP*T P*AP*C)-3')
  • PROTEIN (TRP REPRESSOR)
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / TRANSCRIPTION-DNA COMPLEX
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
TRYPTOPHAN / DNA / DNA (> 10) / Trp operon repressor
Similarity search - Component
Biological speciesEscherichia coli str. K12 substr. (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsOtwinowski, Z. / Schevitz, R.W. / Zhang, R.-G. / Lawson, C.L. / Joachimiak, A. / Marmorstein, R. / Luisi, B.F. / Sigler, P.B.
Citation
Journal: Nature / Year: 1988
Title: Crystal structure of trp repressor/operator complex at atomic resolution.
Authors: Otwinowski, Z. / Schevitz, R.W. / Zhang, R.G. / Lawson, C.L. / Joachimiak, A. / Marmorstein, R.Q. / Luisi, B.F. / Sigler, P.B.
#1: Journal: J.Biol.Chem. / Year: 1987
Title: Crystal of the Trp Repressor-Operator Complex Suitable for X-Ray Diffraction Analysis
Authors: Joachimiak, A. / Marmorstein, R. / Schevitz, R. / Mandecki, W. / Fox, J.L. / Sigler, P.B.
History
DepositionAug 30, 1992Deposition site: BNL / Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3May 13, 2020Group: Data collection / Database references / Structure summary
Category: audit_author / struct_biol / struct_ref_seq_dif / Item: _audit_author.name / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
I: DNA (5'-D(*TP*GP*TP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*TP*AP*GP*T P*AP*C)-3')
J: DNA (5'-D(*TP*GP*TP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*TP*AP*GP*T P*AP*C)-3')
K: DNA (5'-D(*TP*GP*TP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*TP*AP*GP*T P*AP*C)-3')
L: DNA (5'-D(*TP*GP*TP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*TP*AP*GP*T P*AP*C)-3')
A: PROTEIN (TRP REPRESSOR)
C: PROTEIN (TRP REPRESSOR)
E: PROTEIN (TRP REPRESSOR)
G: PROTEIN (TRP REPRESSOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,57712
Polymers72,7608
Non-polymers8174
Water10,305572
1
I: DNA (5'-D(*TP*GP*TP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*TP*AP*GP*T P*AP*C)-3')
J: DNA (5'-D(*TP*GP*TP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*TP*AP*GP*T P*AP*C)-3')
A: PROTEIN (TRP REPRESSOR)
C: PROTEIN (TRP REPRESSOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7886
Polymers36,3804
Non-polymers4082
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
K: DNA (5'-D(*TP*GP*TP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*TP*AP*GP*T P*AP*C)-3')
L: DNA (5'-D(*TP*GP*TP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*TP*AP*GP*T P*AP*C)-3')
E: PROTEIN (TRP REPRESSOR)
G: PROTEIN (TRP REPRESSOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7886
Polymers36,3804
Non-polymers4082
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.650, 72.430, 107.390
Angle α, β, γ (deg.)90.00, 94.96, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE NON-CRYSTALLOGRAPHIC SYMMETRY OF THE STRUCTURE IS NOT EXACT AND THE DEPARTURES FROM THE NON-CRYSTALLOGRAPHIC FOUR-FOLD SYMMETRY DO NOT SEEM TO BE FUNCTIONALLY SIGNIFICANT. TRP REPRESSOR IS A STABLE DIMERIC PROTEIN. ANY ANALYSIS OF OF THIS STRUCTURE REQUIRES THAT A FULL DIMER BE LOOKED AT ONE TIME. THE COORDINATES CONTAIN TWO DIMERS. THE COMPLEX IS MADE BY FOLLOWING CHAIN NUMBERS. COMPLEX 1: A,B,C,D,I,J; COMPLEX 2: E,F,G,H,K,L.

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Components

#1: DNA chain
DNA (5'-D(*TP*GP*TP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*TP*AP*GP*T P*AP*C)-3')


Mass: 5818.796 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Protein
PROTEIN (TRP REPRESSOR)


Mass: 12371.115 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K12 substr. (bacteria)
Species: Escherichia coli / Strain: W3110 / References: UniProt: P0A881
#3: Chemical
ChemComp-TRP / TRYPTOPHAN / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H12N2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 572 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE REGULATORY COFACTOR TRYPTOPHAN, ONE PER MONOMER IS
Sequence detailsSEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: TRPR_ECOLI SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE GLN 14 GLU A 14 GLN 14 GLU C 14 GLN 14 GLU E 14

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.51 %
Crystal growMethod: vapor diffusion / Details: VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NACLSodium chloride11
4CACL211
5NA CACODYLATE11
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDChemical formulaSol-ID
250 mM1NaClreservoir
311 mM1CaCl2reservoir
135 %2,4-dimethyl pentanediol1reservoir
410 mMcacodylate1reservoir
51

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 10 Å / Num. all: 26050 / % possible obs: 87.3 % / Rmerge(I) obs: 0.11

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.9→10 Å
Details: THE CRYSTALLOGRAPHIC TEMPERATURE FACTORS OF THE FIRST TWO PROTEIN AND DNA CHAINS ARE LOWER THAN THE SUBSEQUENT TWO; CONSEQUENTLY THE STRUCTURE OF THE FIRST TWO CHAINS IS MORE ACCURATELY DEFINED.
RfactorNum. reflection
obs0.167 22726
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3205 1544 52 572 5373
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_angle_d1.3
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 10 Å / Rfactor obs: 0.249 / Rfactor Rwork: 0.249
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.3

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