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- PDB-2p19: Crystal structure of bacterial regulatory protein of gntR family ... -

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Basic information

Entry
Database: PDB / ID: 2p19
TitleCrystal structure of bacterial regulatory protein of gntR family from Corynebacterium glutamicum
ComponentsTranscriptional regulator
KeywordsTRANSCRIPTION / Bacterial regulatory protein / gntR family / MCSG / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / 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 / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / GntR-type HTH domain profile. ...UTRA / UbiC transcription regulator-associated / UTRA domain / : / Chorismate lyase / Chorismate lyase-like / Chorismate pyruvate-lyase/UbiC transcription regulator-associated domain superfamily / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcriptional regulators
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsZhang, R. / Zhou, M. / Gu, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of Bacterial regulatory protein of gntR family from Corynebacterium glutamicum
Authors: Zhang, R. / Zhou, M. / Gu, M. / Joachimiak, A.
History
DepositionMar 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator
B: Transcriptional regulator
C: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)48,7283
Polymers48,7283
Non-polymers00
Water9,116506
1
A: Transcriptional regulator
C: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)32,4852
Polymers32,4852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-7 kcal/mol
Surface area15390 Å2
MethodPISA
2
B: Transcriptional regulator

B: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)32,4852
Polymers32,4852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Unit cell
Length a, b, c (Å)106.418, 106.418, 225.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsThis protein may exist as monomer

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Components

#1: Protein Transcriptional regulator / Bacterial regulatory protein / gntR family


Mass: 16242.502 Da / Num. of mol.: 3 / Fragment: Residues 105-253
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Strain: DSM 20300, JCM 1318, LMG 3730, NCIMB 10025 / Gene: Cgl0157, cg0196 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8NTZ4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / 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: 3.79 Å3/Da / Density % sol: 67.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.1M di-Ammonium tartrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 26, 2007 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 42476 / Num. obs: 42209 / % possible obs: 99.37 % / Observed criterion σ(I): 2 / Redundancy: 23.5 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 35.77
Reflection shellResolution: 2.1→2.158 Å / Redundancy: 19.7 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 4.58 / Num. unique all: 3249 / % possible all: 97.69

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→48.17 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.289 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.145 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21874 2237 5 %RANDOM
Rwork0.17789 ---
all0.17991 42209 --
obs0.17991 42209 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.64 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å20.59 Å20 Å2
2--1.19 Å20 Å2
3----1.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.042 Å0.038 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.1→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3344 0 0 506 3850
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223390
X-RAY DIFFRACTIONr_angle_refined_deg1.3212.0034593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6945437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.79923.826149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00215601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6531534
X-RAY DIFFRACTIONr_chiral_restr0.0910.2547
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022528
X-RAY DIFFRACTIONr_nbd_refined0.2010.21397
X-RAY DIFFRACTIONr_nbtor_refined0.2960.22326
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2388
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.2106
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.227
X-RAY DIFFRACTIONr_mcbond_it0.8071.52247
X-RAY DIFFRACTIONr_mcangle_it1.38923489
X-RAY DIFFRACTIONr_scbond_it2.56931263
X-RAY DIFFRACTIONr_scangle_it3.9944.51104
LS refinement shellResolution: 2.1→2.158 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 173 -
Rwork0.193 3001 -
obs-3174 97.69 %
Refinement TLS params.Method: refined / Origin x: 41.47 Å / Origin y: 37.956 Å / Origin z: 2.313 Å
111213212223313233
T-0.0054 Å2-0.01 Å20.0073 Å2--0.0188 Å20.0119 Å2---0.0577 Å2
L0.2688 °2-0.1542 °20.0487 °2-0.2744 °2-0.0213 °2--0.4938 °2
S0.0401 Å °-0.0047 Å °0.0099 Å °-0.0567 Å °0.0004 Å °-0.0029 Å °-0.0138 Å °-0.0432 Å °-0.0405 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 502 - 50
2X-RAY DIFFRACTION1AA51 - 10051 - 100
3X-RAY DIFFRACTION1AA101 - 149101 - 149
4X-RAY DIFFRACTION1BB7 - 507 - 50
5X-RAY DIFFRACTION1BB51 - 10051 - 100
6X-RAY DIFFRACTION1BB101 - 148101 - 148
7X-RAY DIFFRACTION1CC1 - 501 - 50
8X-RAY DIFFRACTION1CC51 - 10051 - 100
9X-RAY DIFFRACTION1CC101 - 148101 - 148

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