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- PDB-1mi7: Crystal Structure of Domain Swapped trp Aporepressor in 30%(v/v) ... -

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Basic information

Entry
Database: PDB / ID: 1mi7
TitleCrystal Structure of Domain Swapped trp Aporepressor in 30%(v/v) Isopropanol
ComponentsTrp operon repressor
KeywordsTRANSCRIPTION / DOMAIN SWAPPING / DNA BINDING PROTEIN / ALCOHOL INDUCED CONFORMATIONAL REARRANGEMENT
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
ISOPROPYL ALCOHOL / Trp operon repressor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLawson, C.L. / Benoff, B. / Berger, T. / Berman, H.M. / Carey, J.
CitationJournal: Structure / Year: 2004
Title: E. coli trp repressor forms a domain-swapped array in aqueous alcohol.
Authors: Lawson, C.L. / Benoff, B. / Berger, T. / Berman, H.M. / Carey, J.
History
DepositionAug 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: 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_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
Remark 600HETEROGEN HOH ATOM COORDINATES DEFINE SOLVENT MOLECULES THAT MAY BE EITHER WATER OR ISOPROPANOL. OF ...HETEROGEN HOH ATOM COORDINATES DEFINE SOLVENT MOLECULES THAT MAY BE EITHER WATER OR ISOPROPANOL. OF 47 SOLVENT POSITIONS LABELLED AS WATER (HOH), MORE THAN HALF ARE SUSPECTED TO BE AT LEAST PARTIALLY OCCUPIED BY ISOPROPANOL, BASED EITHER ON LOW B-FACTOR OR RELATIVELY LONG CONTACT DISTANCES TO PROTEIN ATOMS. ONLY IN ONE CASE COULD SOLVENT BE UNAMBIGUOUSLY ASSIGNED AS ISOPROPANOL BASED ON ELECTRON DENSITY SHAPE (IOH 200).
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL UNIT REPRESENTS A PORTION OF THE DOMAIN-SWAPPED THREE DIMENSIONAL ARRAY

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
R: Trp operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2992
Polymers12,2391
Non-polymers601
Water84747
1
R: Trp operon repressor
hetero molecules

R: Trp operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5984
Polymers24,4782
Non-polymers1202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area3080 Å2
ΔGint-17 kcal/mol
Surface area16120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.310, 85.310, 113.968
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsCRYSTAL LATTICE: THE BIOLOGICAL UNIT REPRESENTS A PORTION OF THE DOMAIN-SWAPPED THREE DIMENSIONAL ARRAY The crystal lattice is generated almost entirely by extensive, branched domain swapping of dimer precursors, so the minimal relevant assembly might be considered to be the entire crystal. To generate this assembly, use the full complement of crystallographic symmetry operators for space group P6(1)22. / ASYMMETRIC UNIT CONTACTS: to generate the nine crystallographic symmetry-related chains that make crystal contacts to the deposited asymmetric unit, use the following operators: X-Y,X,Z+1/6 dx= 1 dy= 1 dz= 0; -Y,X-Y,Z+1/3 dx= 1 dy= 1 dz= 0; -X+Y,-X,Z+2/3 dx= 0 dy= 1 dz=-1; Y,-X+Y,Z+5/6 dx=-1 dy= 0 dz=-1; Y,X,-Z+1/3 dx=-1 dy= 0 dz= 0; Y,X,-Z+1/3 dx= 0 dy= 1 dz= 0; -Y,-X,-Z+5/6 dx= 0 dy= 0 dz=-1; -X+Y,Y,-Z+1/2 dx= 0 dy= 0 dz= 0; X,X-Y,-Z+1/6 dx= 0 dy= 1 dz= 0.

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Components

#1: Protein Trp operon repressor


Mass: 12238.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: aporepressor / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trpR / Plasmid: pET13a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P0A881
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 4.89 Å3/Da / Density % sol: 74.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Na HEPES, 100 mM sodium chloride, 30%(v/v) isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15-20 mg/mlprotein1drop
230-35 %(v/v)isopropanol1reservoir
3100 mMsodium HEPES1reservoirpH7.5
4100 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Apr 24, 2001
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 8304 / Num. obs: 8304 / % possible obs: 92.5 % / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Biso Wilson estimate: 61.3 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 24.1
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 2.6 / Num. unique all: 526 / % possible all: 61
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 67359
Reflection shell
*PLUS
% possible obs: 61 % / Num. unique obs: 526 / Num. measured obs: 1340

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WRP BIOLOGICAL DIMER

2wrp
PDB Unreleased entry


Resolution: 2.5→74.54 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.882 / SU B: 10.109 / SU ML: 0.212 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC, WITH TLS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.305 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28756 455 5.6 %RANDOM, 5.5%
Rwork0.25308 ---
obs0.25505 7722 91.38 %-
all-7722 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.215 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å2-0.47 Å20 Å2
2---0.93 Å20 Å2
3---1.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.432 Å / Luzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 2.5→74.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms830 0 4 47 881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021845
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5771.981141
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6625102
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0940.2130
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02632
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.240.2346
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.238
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.8344516
X-RAY DIFFRACTIONr_mcangle_it3.0125823
X-RAY DIFFRACTIONr_scbond_it3.4275329
X-RAY DIFFRACTIONr_scangle_it5.1785318
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.59 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.338 29 -
Rwork0.297 464 -
obs-522 61 %
Refinement TLS params.Method: refined / Origin x: -15.873 Å / Origin y: 43.447 Å / Origin z: 17.537 Å
111213212223313233
T0.4072 Å20.069 Å2-0.1194 Å2-0.5041 Å2-0.1386 Å2--0.083 Å2
L6.8461 °22.2165 °23.5787 °2-1.0296 °20.5586 °2--1.3732 °2
S0.2773 Å °0.1292 Å °-0.7327 Å °-0.0937 Å °-0.0971 Å °-0.2004 Å °0.064 Å °-0.0783 Å °-0.1801 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1RA3 - 1052 - 104
2X-RAY DIFFRACTION1RB - A2001
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 50 Å / Rfactor Rfree: 0.315 / Rfactor Rwork: 0.274
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.58
LS refinement shell
*PLUS
Rfactor Rfree: 0.359 / Rfactor Rwork: 0.353

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