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- PDB-3ddv: The crystal structure of the transcriptional regulator (GntR fami... -

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Basic information

Entry
Database: PDB / ID: 3ddv
TitleThe crystal structure of the transcriptional regulator (GntR family) from Enterococcus faecalis V583
ComponentsTranscriptional regulator (GntR family)
Keywordstranscription regulator / Transcriptional regulator (GntR family / Structure genomics / PSI2 / MCSG / Structural Genomics / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
Similarity search - Function
UTRA / UbiC transcription regulator-associated / UTRA domain / Chorismate lyase / Chorismate lyase-like / Chorismate pyruvate-lyase/UbiC transcription regulator-associated domain superfamily / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family ...UTRA / UbiC transcription regulator-associated / UTRA domain / Chorismate lyase / Chorismate lyase-like / Chorismate pyruvate-lyase/UbiC transcription regulator-associated domain superfamily / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcriptional regulator, GntR family
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsZhang, R. / Zhou, M. / Bargassa, M. / Otwinowski, Z. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the transcriptional regulator (GntR family) from Enterococcus faecalis V583
Authors: Zhang, R. / Zhou, M. / Bargassa, M. / Otwinowski, Z. / Joachimiak, A.
History
DepositionJun 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 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

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator (GntR family)
B: Transcriptional regulator (GntR family)
C: Transcriptional regulator (GntR family)
D: Transcriptional regulator (GntR family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4637
Polymers66,3914
Non-polymers733
Water1,15364
1
A: Transcriptional regulator (GntR family)
B: Transcriptional regulator (GntR family)
hetero molecules

C: Transcriptional regulator (GntR family)
D: Transcriptional regulator (GntR family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4637
Polymers66,3914
Non-polymers733
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_565x-y,-y+1,-z+1/31
Buried area6720 Å2
ΔGint-44 kcal/mol
Surface area25200 Å2
MethodPISA
2
A: Transcriptional regulator (GntR family)
B: Transcriptional regulator (GntR family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2444
Polymers33,1952
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-20 kcal/mol
Surface area14070 Å2
MethodPISA
3
C: Transcriptional regulator (GntR family)
D: Transcriptional regulator (GntR family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2203
Polymers33,1952
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-16 kcal/mol
Surface area13790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.153, 86.153, 240.059
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThis protein existed as dimer. The deposited MolA/MolB and MolC/MolD are two dimers in the asymmtric unit.

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Components

#1: Protein
Transcriptional regulator (GntR family)


Mass: 16597.646 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: GI:29343357 / Plasmid: PDM68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q835P8*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.: 64 / 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: 3.87 Å3/Da / Density % sol: 68.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Tris, 2M ammonium sulfate, pH 8.0, 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: Mar 15, 2007 / 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: 2.65→80.06 Å / Num. all: 29406 / Num. obs: 28847 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.4 % / Biso Wilson estimate: 52 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 47.9
Reflection shellResolution: 2.65→2.718 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 1.88 / Num. unique all: 2253 / % possible all: 75.68

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.65→80.06 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 21.355 / SU ML: 0.211 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.338 / ESU R Free: 0.262
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25115 1529 5 %RANDOM
Rwork0.20609 ---
obs0.20828 28847 98.1 %-
all-29406 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.144 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.11 Å20 Å2
2--0.22 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.65→80.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4185 0 3 64 4252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0224273
X-RAY DIFFRACTIONr_bond_other_d0.0010.023013
X-RAY DIFFRACTIONr_angle_refined_deg2.0081.9665759
X-RAY DIFFRACTIONr_angle_other_deg1.02137280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3795512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.18323.239213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.69515756
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.321538
X-RAY DIFFRACTIONr_chiral_restr0.110.2619
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024730
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02928
X-RAY DIFFRACTIONr_nbd_refined0.2330.2841
X-RAY DIFFRACTIONr_nbd_other0.2120.23221
X-RAY DIFFRACTIONr_nbtor_refined0.2020.22112
X-RAY DIFFRACTIONr_nbtor_other0.0990.22563
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2148
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0560.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2210.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3860.23
X-RAY DIFFRACTIONr_mcbond_it1.1651.53241
X-RAY DIFFRACTIONr_mcbond_other0.1561.51034
X-RAY DIFFRACTIONr_mcangle_it1.42924177
X-RAY DIFFRACTIONr_scbond_it2.06331968
X-RAY DIFFRACTIONr_scangle_it3.0644.51582
LS refinement shellResolution: 2.649→2.718 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 83 -
Rwork0.38 1622 -
obs-1705 75.68 %
Refinement TLS params.Method: refined / Origin x: 41.549 Å / Origin y: 28.111 Å / Origin z: 36.145 Å
111213212223313233
T-0.2257 Å20.0054 Å2-0.0203 Å2-0.3714 Å2-0.0188 Å2---0.0185 Å2
L0.2291 °2-0.1819 °20.6752 °2-0.7648 °2-0.2487 °2--2.1234 °2
S0.1845 Å °0.0489 Å °-0.0817 Å °-0.0133 Å °-0.0626 Å °0.0509 Å °0.1112 Å °-0.0193 Å °-0.1218 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 145
2X-RAY DIFFRACTION1B7 - 145
3X-RAY DIFFRACTION1C5 - 145
4X-RAY DIFFRACTION1D7 - 144

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