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- PDB-3g1c: The crystal structure of a TrpR like protein from Eubacterium eli... -

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Basic information

Entry
Database: PDB / ID: 3g1c
TitleThe crystal structure of a TrpR like protein from Eubacterium eligens ATCC 27750
ComponentsThe TrpR like protein from Eubacterium eligens ATCC 27750
Keywordstranscription / DNA binding protein / TrpR like protein / Eubacterium eligens / Structural Genomics / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics / unknown function
Function / homology
Function and homology information


sequence-specific DNA binding / DNA-binding transcription factor activity
Similarity search - Function
TrpR homologue YerC/YecD / TrpR-like / 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
The TrpR like protein from Eubacterium eligens ATCC 27750
Similarity search - Component
Biological speciesEubacterium eligens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsZhang, R. / Hendricks, R. / Freeman, L. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a TrpR like protein from Eubacterium eligens ATCC 27750
Authors: Zhang, R. / Hendricks, R. / Freeman, L. / Babnigg, G. / Joachimiak, A.
History
DepositionJan 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 21, 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

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Assembly

Deposited unit
A: The TrpR like protein from Eubacterium eligens ATCC 27750
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1324
Polymers12,0601
Non-polymers733
Water1,06359
1
A: The TrpR like protein from Eubacterium eligens ATCC 27750
hetero molecules

A: The TrpR like protein from Eubacterium eligens ATCC 27750
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2658
Polymers24,1192
Non-polymers1466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area5860 Å2
ΔGint-69 kcal/mol
Surface area10370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.788, 48.788, 126.477
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe second part of the biological assembly is generated by the two fold axis: -y,-x,-z+1/2

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Components

#1: Protein The TrpR like protein from Eubacterium eligens ATCC 27750


Mass: 12059.517 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eubacterium eligens (bacteria) / Strain: ATCC 27750 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: C4Z2H9*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 3.12 Å3/Da / Density % sol: 60.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH7.5, 0.5M Magnesium formate dihydrate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 3, 2008 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.2→38.63 Å / Num. all: 7945 / Num. obs: 7885 / % possible obs: 99.24 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 15.4 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 31.34
Reflection shellResolution: 2.2→2.257 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 1.28 / Num. unique all: 594 / % possible all: 94.44

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2→38.63 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.544 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1.28 / ESU R: 0.2 / ESU R Free: 0.174
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23657 381 4.6 %RANDOM
Rwork0.20484 ---
obs0.20632 7885 99.24 %-
all-7945 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.638 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å20 Å20 Å2
2--1.72 Å20 Å2
3----3.44 Å2
Refinement stepCycle: LAST / Resolution: 2.2→38.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms787 0 3 59 849
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.022796
X-RAY DIFFRACTIONr_bond_other_d0.0010.02547
X-RAY DIFFRACTIONr_angle_refined_deg1.61.9651069
X-RAY DIFFRACTIONr_angle_other_deg0.90131327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.673596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.95424.41943
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.49615152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.461157
X-RAY DIFFRACTIONr_chiral_restr0.1030.2121
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02884
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02167
X-RAY DIFFRACTIONr_mcbond_it1.0991.5480
X-RAY DIFFRACTIONr_mcbond_other0.2531.5197
X-RAY DIFFRACTIONr_mcangle_it2.1862770
X-RAY DIFFRACTIONr_scbond_it3.3363316
X-RAY DIFFRACTIONr_scangle_it5.6084.5299
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 29 -
Rwork0.245 532 -
obs-561 94.44 %

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