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- PDB-5hpi: Crystal Structure of the Double Mutant of PobR Transcription Fact... -

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Basic information

Entry
Database: PDB / ID: 5hpi
TitleCrystal Structure of the Double Mutant of PobR Transcription Factor Inducer Binding Domain-3-Hydroxy Benzoic Acid complex from Acinetobacter
Componentsp-hydroxybenzoate hydroxylase transcriptional activator
KeywordsTRANSCRIPTION / Transcription factor / ligand binding domain
Function / homology
Function and homology information


3,4-dihydroxybenzoate metabolic process / catabolic process / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Beta-ketoadipate transcriptional regulator, PcaR/PcaU/PobR / helix_turn_helix isocitrate lyase regulation / IclR helix-turn-helix domain / Transcription regulator IclR, N-terminal / Transcription regulator IclR, C-terminal / : / Bacterial transcriptional regulator IclR C-terminal / IclR-type HTH domain profile. / IclR effector binding domain profile. / GAF domain ...Beta-ketoadipate transcriptional regulator, PcaR/PcaU/PobR / helix_turn_helix isocitrate lyase regulation / IclR helix-turn-helix domain / Transcription regulator IclR, N-terminal / Transcription regulator IclR, C-terminal / : / Bacterial transcriptional regulator IclR C-terminal / IclR-type HTH domain profile. / IclR effector binding domain profile. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
3-HYDROXYBENZOIC ACID / p-hydroxybenzoate hydroxylase transcriptional activator
Similarity search - Component
Biological speciesAcinetobacter baylyi str. ADP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.963 Å
AuthorsKim, Y. / Tesar, C. / Jedrejczak, R. / Jha, R. / Strauss, C.E.M. / Joachimiak, A.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: A microbial sensor for organophosphate hydrolysis exploiting an engineered specificity switch in a transcription factor.
Authors: Jha, R.K. / Kern, T.L. / Kim, Y. / Tesar, C. / Jedrzejczak, R. / Joachimiak, A. / Strauss, C.E.
History
DepositionJan 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / entity_src_gen / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: p-hydroxybenzoate hydroxylase transcriptional activator
B: p-hydroxybenzoate hydroxylase transcriptional activator
C: p-hydroxybenzoate hydroxylase transcriptional activator
D: p-hydroxybenzoate hydroxylase transcriptional activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,04516
Polymers79,8264
Non-polymers1,21912
Water23413
1
A: p-hydroxybenzoate hydroxylase transcriptional activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2194
Polymers19,9561
Non-polymers2623
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: p-hydroxybenzoate hydroxylase transcriptional activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3495
Polymers19,9561
Non-polymers3924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: p-hydroxybenzoate hydroxylase transcriptional activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1913
Polymers19,9561
Non-polymers2342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: p-hydroxybenzoate hydroxylase transcriptional activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2874
Polymers19,9561
Non-polymers3303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.490, 125.659, 156.673
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
p-hydroxybenzoate hydroxylase transcriptional activator


Mass: 19956.459 Da / Num. of mol.: 4 / Fragment: UNP residues 96-271 / Mutation: delta-L141, L220V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baylyi str. ADP1 (bacteria)
Gene: pobR, ACIAD1718 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / References: UniProt: Q43992
#2: Chemical
ChemComp-3HB / 3-HYDROXYBENZOIC ACID


Mass: 138.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H6O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.44 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.0 M Lithium Sulfate, 2.0 % (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 25, 2015
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 16803 / % possible obs: 96.2 % / Redundancy: 4.3 % / Biso Wilson estimate: 65.7 Å2 / Rmerge(I) obs: 0.157 / Net I/σ(I): 7.49
Reflection shellResolution: 2.95→3 Å / Redundancy: 4 % / Rmerge(I) obs: 0.827 / Mean I/σ(I) obs: 1.3 / % possible all: 88.9

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Processing

Software
NameVersionClassification
PHENIX(1.10pre_2104: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
SBC-Collectdata collection
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 5HPF

5hpf


Resolution: 2.963→49.013 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2579 817 4.91 %
Rwork0.1967 --
obs0.1998 16651 95.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.5 Å2
Refinement stepCycle: LAST / Resolution: 2.963→49.013 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5439 0 77 13 5529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095638
X-RAY DIFFRACTIONf_angle_d0.9777696
X-RAY DIFFRACTIONf_dihedral_angle_d15.9243407
X-RAY DIFFRACTIONf_chiral_restr0.051930
X-RAY DIFFRACTIONf_plane_restr0.006988
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9625-3.14810.31141380.26942318X-RAY DIFFRACTION85
3.1481-3.39110.34431230.25062565X-RAY DIFFRACTION94
3.3911-3.73230.29791270.21692711X-RAY DIFFRACTION98
3.7323-4.27210.25571390.18982724X-RAY DIFFRACTION99
4.2721-5.38130.22761520.17272721X-RAY DIFFRACTION98
5.3813-49.01930.2331380.17732795X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.0895-0.71081.1438.59430.43595.8061-0.2640.03610.22240.8858-0.22030.9340.3665-1.04740.72770.473-0.03760.00730.6283-0.06640.4986-51.3158-14.9733-13.4699
21.8161-1.47020.69112.5557-2.78597.35941.1393-0.1801-1.25250.25670.07781.56351.6483-0.0733-1.16991.0313-0.0072-0.20670.49970.11080.8829-48.9233-24.68-14.4856
31.5223-2.8511-0.71578.1261-2.93566.8160.49520.1608-1.033-0.41640.74111.76640.4859-1.1115-0.34130.9894-0.133-0.07090.67510.10221.3672-43.6157-31.4073-13.5289
45.11-1.74450.79566.56470.27025.73490.06-0.0133-0.1057-0.24930.0787-0.30390.17660.082-0.1310.4192-0.01190.03880.40280.03660.3298-33.8589-22.4067-14.6736
53.9997-2.15640.21844.37881.10595.1039-0.103-0.3924-0.15390.58730.1058-0.41640.38030.2887-0.00340.50380.01480.0180.49430.0610.48-17.5501-25.2435-32.7442
64.3078-1.6898-0.5968.04413.62295.5461-0.07490.145-0.0828-0.43160.0311-0.23240.04320.0670.05880.39960.0338-0.00030.38590.06230.4438-17.3463-23.4662-47.2789
74.3163-0.534-4.19693.81753.54166.81710.1180.1922-0.3349-0.2669-0.4102-1.26270.04570.2352-0.03730.5376-0.00040.02870.4877-0.0430.5335-17.8819-0.0274-27.103
84.8565-0.0396-1.83845.83060.15696.33570.40850.44480.6504-0.99120.2516-1.0115-2.62680.6645-0.47760.75270.0872-0.16540.4140.03150.5272-17.7058.6994-27.9935
92.96421.0661-3.92245.30563.00459.27331.3340.3407-0.3289-0.2807-0.3627-1.5234-2.08750.9112-0.8280.85550.00830.02370.6-0.07380.7102-20.978813.7904-23.0586
104.70121.8394-0.1237.4770.71186.10170.0223-0.97610.78431.34260.02540.77640.16720.0988-0.0210.49920.0215-0.05260.5143-0.10730.366-30.546210.6045-9.108
116.0675-1.06790.97764.4091.07425.5710.2231-0.086-0.0779-0.1136-0.05980.12980.07220.2015-0.12230.4191-0.0606-0.01320.45310.00380.5036-27.60740.851-23.2884
129.03393.06440.62717.85222.40883.3383-0.5872-0.8051-0.8062-0.758-1.3121-0.398-0.62620.65831.09610.4217-0.0105-0.0630.54020.26360.6112-31.8147-1.1125-63.8602
134.3124-0.2052.51014.7834-0.46855.6333-0.04140.2160.94490.0593-0.055-0.3234-0.97380.14570.22240.765-0.0932-0.07910.40440.02010.4825-31.08648.5118-60.8973
145.94212.1937-1.12632.86421.71632.4454-0.52511.35920.6148-0.19520.1132-0.6679-1.06390.10880.20520.5594-0.04410.10040.7160.09220.7413-13.908612.1782-55.4162
156.03870.7588-0.0162.51691.35017.8396-0.25-0.33330.92772.01950.3011-0.5477-0.46340.90190.21070.6436-0.0525-0.06540.6506-0.03750.6522-13.958712.4094-45.2688
166.3045-1.169-0.54093.69373.59133.56420.09070.25040.9739-0.93590.0557-0.6241-0.30210.0812-0.03590.59460.003-0.07370.65830.06960.4915-22.16994.999-51.7218
175.74215.3360.82358.6071-2.61098.3003-0.4238-0.0049-0.45190.00410.03991.2120.1842-0.14540.17140.3125-0.00370.03230.4699-0.02860.6232-28.3936-0.6844-51.4809
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 96 through 113 )
2X-RAY DIFFRACTION2chain 'A' and (resid 114 through 143 )
3X-RAY DIFFRACTION3chain 'A' and (resid 144 through 159 )
4X-RAY DIFFRACTION4chain 'A' and (resid 160 through 271 )
5X-RAY DIFFRACTION5chain 'B' and (resid 99 through 159 )
6X-RAY DIFFRACTION6chain 'B' and (resid 160 through 271 )
7X-RAY DIFFRACTION7chain 'C' and (resid 97 through 123 )
8X-RAY DIFFRACTION8chain 'C' and (resid 124 through 143 )
9X-RAY DIFFRACTION9chain 'C' and (resid 144 through 159 )
10X-RAY DIFFRACTION10chain 'C' and (resid 160 through 207 )
11X-RAY DIFFRACTION11chain 'C' and (resid 208 through 271 )
12X-RAY DIFFRACTION12chain 'D' and (resid 96 through 113 )
13X-RAY DIFFRACTION13chain 'D' and (resid 114 through 143 )
14X-RAY DIFFRACTION14chain 'D' and (resid 149 through 181 )
15X-RAY DIFFRACTION15chain 'D' and (resid 182 through 207 )
16X-RAY DIFFRACTION16chain 'D' and (resid 208 through 233 )
17X-RAY DIFFRACTION17chain 'D' and (resid 234 through 271 )

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