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- PDB-4tv7: Crystal structure of Bacillus subtilis GabR at 2.05 Angstroms res... -

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Basic information

Entry
Database: PDB / ID: 4tv7
TitleCrystal structure of Bacillus subtilis GabR at 2.05 Angstroms resolution
ComponentsHTH-type transcriptional regulatory protein GabR
KeywordsTRANSCRIPTION / transcriptional regulator
Function / homology
Function and homology information


transaminase activity / biosynthetic process / pyridoxal phosphate binding / DNA-binding transcription factor activity / DNA binding
Similarity search - Function
GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Pyridoxal phosphate-dependent transferase, major domain ...GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
HTH-type transcriptional regulatory protein GabR
Similarity search - Component
Biological speciesBacillus subtilis 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / MIR / Resolution: 2.05 Å
AuthorsGoto, M. / Okuda, K. / Yoshimura, T.
CitationJournal: Mol. Microbiol. / Year: 2015
Title: Role of the aminotransferase domain in Bacillus subtilis GabR, a pyridoxal 5'-phosphate-dependent transcriptional regulator
Authors: Okuda, K. / Kato, S. / Ito, T. / Shiraki, S. / Kawase, Y. / Goto, M. / Kawashima, S. / Hemmi, H. / Fukada, H. / Yoshimura, T.
History
DepositionJun 26, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references
Revision 1.2Jan 29, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HTH-type transcriptional regulatory protein GabR
B: HTH-type transcriptional regulatory protein GabR
C: HTH-type transcriptional regulatory protein GabR
D: HTH-type transcriptional regulatory protein GabR


Theoretical massNumber of molelcules
Total (without water)221,8734
Polymers221,8734
Non-polymers00
Water10,142563
1
A: HTH-type transcriptional regulatory protein GabR
B: HTH-type transcriptional regulatory protein GabR


Theoretical massNumber of molelcules
Total (without water)110,9362
Polymers110,9362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7240 Å2
ΔGint-36 kcal/mol
Surface area36450 Å2
MethodPISA
2
C: HTH-type transcriptional regulatory protein GabR
D: HTH-type transcriptional regulatory protein GabR


Theoretical massNumber of molelcules
Total (without water)110,9362
Polymers110,9362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7940 Å2
ΔGint-28 kcal/mol
Surface area38020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.831, 101.556, 212.987
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
HTH-type transcriptional regulatory protein GabR


Mass: 55468.215 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Lys312 makes a schiff base with PLP. / Source: (gene. exp.) Bacillus subtilis 168 (bacteria) / Gene: gabR, ycnF, BSU03890 / Plasmid: pBAD18 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: P94426
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 563 / 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: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 1000, PEG 400, ethyleneglycol, calcium acetate, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 130131 / % possible obs: 97.3 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.059 / Χ2: 1.86 / Net I/av σ(I): 45.119 / Net I/σ(I): 16.2 / Num. measured all: 797244
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.05-2.095.40.5863021.22395.6
2.09-2.125.70.49964271.24497
2.12-2.1660.44264441.27897.3
2.16-2.216.10.37864551.29297.5
2.21-2.266.30.32364601.3197.9
2.26-2.316.30.27664801.35797.9
2.31-2.376.30.22864911.41498.1
2.37-2.436.30.18965491.45998.3
2.43-2.56.40.15964991.50998.4
2.5-2.586.40.13665271.55498.3
2.58-2.686.30.11365231.66498.1
2.68-2.786.30.09465871.75999
2.78-2.916.30.0865671.89698.4
2.91-3.066.30.0766322.00599
3.06-3.256.30.0666092.2499
3.25-3.516.20.05266352.43998.7
3.51-3.866.20.0566612.79499.2
3.86-4.4260.04766823.03798.3
4.42-5.565.80.04666353.09197.4
5.56-505.70.03959662.65883.8

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Phasing

PhasingMethod: MIR

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SOLVEphasing
RESOLVE2.13phasing
REFMACrefmac_5.7.0032refinement
PDB_EXTRACT3.14data extraction
RESOLVEmodel building
REFMACrefinement
SOLVEmodel building
REFMAC5refinement
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→47.67 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.941 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28442 6564 5 %RANDOM
Rwork0.23111 ---
obs0.23381 123479 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.039 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å2-0 Å2-0 Å2
2---0.4 Å20 Å2
3----0.19 Å2
Refinement stepCycle: 1 / Resolution: 2.05→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13936 0 0 563 14499
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01914203
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4491.97619196
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.94151738
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52523.772639
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.522152465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2831599
X-RAY DIFFRACTIONr_chiral_restr0.0980.22145
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110628
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4255.1957027
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.9027.7618740
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.0445.4587176
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.51543.75922187
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.049→2.102 Å / Total num. of bins used: 20 / WRfactor Rwork: 0.348
RfactorNum. reflection% reflection
Rfree0.335 470 -
Rwork0.291 8898 -
obs--95.85 %

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