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- PDB-1jhg: TRP REPRESSOR MUTANT V58I -

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Basic information

Entry
Database: PDB / ID: 1jhg
TitleTRP REPRESSOR MUTANT V58I
ComponentsTRP OPERON REPRESSOR
KeywordsDNA BINDING PROTEIN / REGULATORY PROTEIN-PEPTIDE 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
PHOSPHATE ION / TRYPTOPHAN / Trp operon repressor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS TO PDB ENTRY 2WRP / Resolution: 1.3 Å
AuthorsLawson, C.L.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: An atomic view of the L-tryptophan binding site of trp repressor.
Authors: Lawson, C.L.
#1: Journal: Biological Structure and Dynamics: Proceedings of the Ninth Conversation in the Discipline Biomolecular Stereodynamics, Held at the State University of New York at Albany, June 20-24, 1995
Year: 1996
Title: Structural Consequences of Twp Methyl Additions in the Escherichia Coli Trp Repressor L-Tryptophan Binding Pocket
Authors: Lawson, C.L.
History
DepositionJul 19, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3May 21, 2014Group: Database references
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRP OPERON REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8773
Polymers11,5781
Non-polymers2992
Water2,144119
1
A: TRP OPERON REPRESSOR
hetero molecules

A: TRP OPERON REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7556
Polymers23,1572
Non-polymers5984
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4780 Å2
ΔGint-45 kcal/mol
Surface area11500 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)53.536, 32.789, 53.385
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-308-

HOH

21A-312-

HOH

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Components

#1: Protein TRP OPERON REPRESSOR


Mass: 11578.260 Da / Num. of mol.: 1 / Mutation: CHAIN A, V58I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Description: I58 TRP REPRESSOR WAS GROWN IN ESCHERICHIA COLI STRAIN BL21 (DE3) USING T7 EXPRESSION SYSTEM VECTORS;
Cell line: BL21 / Plasmid: PET13A / Species (production host): Escherichia coli / Cell (production host): CYTOPLASM / Gene (production host): TRPRI58 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P0A881
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-TRP / TRYPTOPHAN / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTWO TORSIONAL ANGLES IN THE L-TRYPTOPHAN BINDING POCKET HAVE DISTINCTLY NON-IDEAL GEOMETRY: CHI1 OF ...TWO TORSIONAL ANGLES IN THE L-TRYPTOPHAN BINDING POCKET HAVE DISTINCTLY NON-IDEAL GEOMETRY: CHI1 OF THE L-TRYPTOPHAN LIGAND (-155 DEGREES) OMEGA OF THE LEU 41 - MET 42 PEPTIDE BOND (168 DEGREES) REFERENCE 1 DISCUSSES THE POSSIBLE BIOLOGICAL SIGNIFICANCE OF THESE DISTORTIONS.

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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: 1.9 Å3/Da / Density % sol: 37 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5
Details: HANGING DROP VAPOR DIFFUSION 2.0 M SODIUM PHOSPHATE, PH 5.0 600 MM AMMONIUM CHLORIDE 5 MM L-TRYPTOPHAN, vapor diffusion - hanging drop
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.0 Msodium phosphate1reservoir
2600 mMammonium chloride1reservoir
31-5 mML-trp1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.99
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Aug 1, 1994
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. obs: 86193 / % possible obs: 97.4 % / Observed criterion σ(I): 0.25 / Redundancy: 3.6 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 28.4
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.167 / Mean I/σ(I) obs: 20 / % possible all: 94
Reflection shell
*PLUS
% possible obs: 94 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-93model building
SHELXL-93refinement
SHELXL-93phasing
RefinementMethod to determine structure: ISOMORPHOUS TO PDB ENTRY 2WRP
Resolution: 1.3→30 Å / Num. parameters: 8337 / Num. restraintsaints: 2568 / Cross valid method: FREE R / Stereochemistry target values: ENGH AND HUBER
Details: RIDING HYDROGEN ATOM OPTION OF SHELXL USED, ANISOTROPIC TEMPERATURE FACTORS REFINED BUT NOT INCLUDED IN THE DEPOSITION. SOME SIDE-CHAIN, SOLVENT, AND ALL PHOSPHATE ATOMS HAVE PARTIAL ...Details: RIDING HYDROGEN ATOM OPTION OF SHELXL USED, ANISOTROPIC TEMPERATURE FACTORS REFINED BUT NOT INCLUDED IN THE DEPOSITION. SOME SIDE-CHAIN, SOLVENT, AND ALL PHOSPHATE ATOMS HAVE PARTIAL OCCUPANCIES. APPARENT "SHORT" INTERATOMIC DISTANCES INDICATE POSITIONS IN THE CRYSTAL WHERE THERE ARE AT LEAST TWO ALTERNATE MODELS.
RfactorNum. reflection% reflectionSelection details
Rfree0.172 2334 10 %EVERY 10TH REFLECTION
all0.1268 23349 --
obs0.1218 -97.4 %-
Solvent computationSolvent model: SWAT 7.731 2.0 (BABINET'S PRINCIPLE)
Refine analyzeNum. disordered residues: 15 / Occupancy sum hydrogen: 4248 / Occupancy sum non hydrogen: 3504
Refinement stepCycle: LAST / Resolution: 1.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms804 0 20 119 943
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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