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- PDB-1trr: TANDEM BINDING IN CRYSTALS OF A TRP REPRESSOR/OPERATOR HALF-SITE ... -

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Basic information

Entry
Database: PDB / ID: 1trr
TitleTANDEM BINDING IN CRYSTALS OF A TRP REPRESSOR/OPERATOR HALF-SITE COMPLEX
Components
  • DNA (5'-D(*AP*GP*CP*GP*TP*AP*CP*TP*AP*GP*TP*AP*CP*GP*CP*T)-3')
  • PROTEIN (TRP REPRESSOR)
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / 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 (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsLawson, C.L. / Carey, J.
Citation
Journal: Nature / Year: 1993
Title: Tandem binding in crystals of a trp repressor/operator half-site complex.
Authors: Lawson, C.L. / Carey, J.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Cocrystals of E. Coli Trp Repressor Bound to an Alternative Operator DNA Sequence
Authors: Carey, J. / Combatti, N. / Lewis, D.E.A. / Lawson, C.L.
History
DepositionOct 21, 1993Deposition site: BNL / Processing site: BNL
Revision 1.0Oct 21, 1993Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
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_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
C: DNA (5'-D(*AP*GP*CP*GP*TP*AP*CP*TP*AP*GP*TP*AP*CP*GP*CP*T)-3')
F: DNA (5'-D(*AP*GP*CP*GP*TP*AP*CP*TP*AP*GP*TP*AP*CP*GP*CP*T)-3')
I: DNA (5'-D(*AP*GP*CP*GP*TP*AP*CP*TP*AP*GP*TP*AP*CP*GP*CP*T)-3')
L: DNA (5'-D(*AP*GP*CP*GP*TP*AP*CP*TP*AP*GP*TP*AP*CP*GP*CP*T)-3')
A: PROTEIN (TRP REPRESSOR)
B: PROTEIN (TRP REPRESSOR)
D: PROTEIN (TRP REPRESSOR)
E: PROTEIN (TRP REPRESSOR)
G: PROTEIN (TRP REPRESSOR)
H: PROTEIN (TRP REPRESSOR)
J: PROTEIN (TRP REPRESSOR)
K: PROTEIN (TRP REPRESSOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,14620
Polymers117,51212
Non-polymers1,6348
Water3,459192
1
C: DNA (5'-D(*AP*GP*CP*GP*TP*AP*CP*TP*AP*GP*TP*AP*CP*GP*CP*T)-3')
I: DNA (5'-D(*AP*GP*CP*GP*TP*AP*CP*TP*AP*GP*TP*AP*CP*GP*CP*T)-3')
A: PROTEIN (TRP REPRESSOR)
B: PROTEIN (TRP REPRESSOR)
G: PROTEIN (TRP REPRESSOR)
H: PROTEIN (TRP REPRESSOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,57310
Polymers58,7566
Non-polymers8174
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: DNA (5'-D(*AP*GP*CP*GP*TP*AP*CP*TP*AP*GP*TP*AP*CP*GP*CP*T)-3')
L: DNA (5'-D(*AP*GP*CP*GP*TP*AP*CP*TP*AP*GP*TP*AP*CP*GP*CP*T)-3')
D: PROTEIN (TRP REPRESSOR)
E: PROTEIN (TRP REPRESSOR)
J: PROTEIN (TRP REPRESSOR)
K: PROTEIN (TRP REPRESSOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,57310
Polymers58,7566
Non-polymers8174
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.340, 90.160, 58.650
Angle α, β, γ (deg.)90.00, 113.92, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.734887, 0.517158, -0.438735), (0.519035, 0.012497, -0.854661), (-0.436512, -0.855799, -0.277607)33.3388, -21.164, -5.0767
2given(0.463631, -0.000522, 0.886028), (0.000455, -1, -0.000828), (0.886028, 0.000787, -0.463631)44.2771, -42.6917, 26.8159
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX 1* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS G, H, AND I WHEN APPLIED TO CHAINS A, B, AND C, RESPECTIVELY. THE TRANSFORMATION PRESENTED ON *MTRIX 2* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS D, E, F, J, K, AND L WHEN APPLIED TO CHAINS A, B, C, G, H, AND I, RESPECTIVELY.

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Components

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


Mass: 4898.191 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Protein
PROTEIN (TRP REPRESSOR)


Mass: 12239.919 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: 3110 / References: UniProt: P0A881
#3: Chemical
ChemComp-TRP / TRYPTOPHAN / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C11H12N2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / 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

Crystal grow
*PLUS
Temperature: 23 ℃ / pH: 4.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Msodium acetate1reservoir
22.0 Msodium formate1reservoir

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Data collection

DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. all: 30065 / Num. obs: 18723
Reflection
*PLUS
Highest resolution: 2.4 Å / % possible obs: 90.3 % / Rmerge(I) obs: 0.05

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementHighest resolution: 2.4 Å
Details: THE MODEL IS MISSING THREE CARBOXYL-TERMINAL RESIDUES FROM EACH REPRESSOR SUBUNIT (106 - 108) AND RESIDUE 1 OF EACH OLIGONUCLEOTIDE (= UNPAIRED 5' THYMIDINE). THEY ARE NOT SEEN IN ELECTRON ...Details: THE MODEL IS MISSING THREE CARBOXYL-TERMINAL RESIDUES FROM EACH REPRESSOR SUBUNIT (106 - 108) AND RESIDUE 1 OF EACH OLIGONUCLEOTIDE (= UNPAIRED 5' THYMIDINE). THEY ARE NOT SEEN IN ELECTRON DENSITY AND, THEREFORE, ARE PRESUMED TO BE DISORDERED. THE AMINO-TERMINAL ARMS (RESIDUES 2 - 16) OF EACH REPRESSOR SUBUNIT WERE MODELLED INTO FAIRLY POOR BUT NEARLY CONTINUOUS ELECTRON DENSITY. THE ARMS WERE BUILT USING THE MOST CLEARLY DEFINED RESIDUES (PRO 5, TYR 7, AND HIS 16) AS GUIDES. THE LEVEL OF UNCERTAINTY IN SPECIFIC ATOM POSITIONS OF THE ARM IS REFLECTED IN POORER STEREOCHEMISTRY OF RESIDUES 2 - 16 WHEN COMPARED TO THE REST OF THE MODEL.
RfactorNum. reflection
Rwork0.241 -
obs0.241 18723
Refinement stepCycle: LAST / Highest resolution: 2.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6808 1300 0 192 8300
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.86
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Highest resolution: 2.4 Å / Rfactor obs: 0.241
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.86

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