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

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Basic information

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


3,4-dihydroxybenzoate metabolic process / : / positive regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Beta-ketoadipate transcriptional regulator, PcaR/PcaU/PobR / helix_turn_helix isocitrate lyase regulation / Bacterial transcriptional regulator / Transcription regulator IclR, N-terminal / Transcription regulator IclR, C-terminal / IclR helix-turn-helix domain / IclR-type HTH domain profile. / IclR effector binding domain profile. / GAF domain / GAF-like domain superfamily ...Beta-ketoadipate transcriptional regulator, PcaR/PcaU/PobR / helix_turn_helix isocitrate lyase regulation / Bacterial transcriptional regulator / Transcription regulator IclR, N-terminal / Transcription regulator IclR, C-terminal / IclR helix-turn-helix domain / 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
PHOSPHATE ION / p-hydroxybenzoate hydroxylase transcriptional activator
Similarity search - Component
Biological speciesAcinetobacter baylyi str. ADP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.309 Å
AuthorsKim, Y. / Tesar, C. / Jedrejczak, R. / Jha, R. / Strauss, C.E.M. / Joachimiak, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
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 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jun 6, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / citation_author / entity_src_gen
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 / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,83714
Polymers59,8693
Non-polymers96811
Water2,126118
1
A: p-hydroxybenzoate hydroxylase transcriptional activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3315
Polymers19,9561
Non-polymers3744
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)19,9922
Polymers19,9561
Non-polymers351
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)20,5157
Polymers19,9561
Non-polymers5586
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.348, 111.348, 282.174
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein p-hydroxybenzoate hydroxylase transcriptional activator


Mass: 19956.459 Da / Num. of mol.: 3 / 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) / Strain (production host): BL21(DE3) / Variant (production host): magic / References: UniProt: Q43992
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.67 Å3/Da / Density % sol: 66.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 0.1 M sodium/potassium phosphate pH 5.6

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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 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 37742 / % possible obs: 99.8 % / Redundancy: 5 % / Biso Wilson estimate: 46.7 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 13.2
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.849 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX(1.10pre_2104: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
SBC-Collectdata collection
RefinementMethod to determine structure: SAD / Resolution: 2.309→40.375 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.16 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2152 1874 4.97 %
Rwork0.1702 --
obs0.1724 37742 95.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.7 Å2
Refinement stepCycle: LAST / Resolution: 2.309→40.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4128 0 57 118 4303
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084262
X-RAY DIFFRACTIONf_angle_d0.9255814
X-RAY DIFFRACTIONf_dihedral_angle_d15.1632583
X-RAY DIFFRACTIONf_chiral_restr0.054703
X-RAY DIFFRACTIONf_plane_restr0.005741
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3089-2.37140.27911180.2252548X-RAY DIFFRACTION90
2.3714-2.44110.27291190.19922782X-RAY DIFFRACTION98
2.4411-2.51990.21581480.19192772X-RAY DIFFRACTION98
2.5199-2.610.28551480.21132753X-RAY DIFFRACTION98
2.61-2.71440.26881450.20682794X-RAY DIFFRACTION97
2.7144-2.8380.28321480.22222759X-RAY DIFFRACTION97
2.838-2.98750.24341380.20362774X-RAY DIFFRACTION97
2.9875-3.17460.25141490.19532768X-RAY DIFFRACTION97
3.1746-3.41960.2291490.18392762X-RAY DIFFRACTION96
3.4196-3.76350.25091670.16492753X-RAY DIFFRACTION96
3.7635-4.30760.18551470.14282761X-RAY DIFFRACTION95
4.3076-5.4250.16331410.13212795X-RAY DIFFRACTION95
5.425-40.38110.17781570.16112847X-RAY DIFFRACTION92
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)
19.2545-1.9486-1.04588.98210.70538.8959-0.11660.2501-0.92150.6478-0.11680.12981.0314-0.0620.20370.4442-0.0499-0.0070.29520.00880.388110.885-24.619455.8096
23.50552.15491.65424.79550.03481.0436-0.17230.5299-0.3528-0.2010.0107-0.08950.2096-0.00670.13210.35640.0210.04630.370.00270.263711.5885-21.526146.0789
35.7651.05312.07835.3223-0.43724.2478-0.27830.2973-0.2604-0.43560.085-0.02030.40080.39840.15760.39850.05290.10910.3479-0.00760.350820.9024-17.025643.3218
47.08671.30462.98554.27190.29997.95180.0720.59420.1316-0.5199-0.3781-1.28080.4531.65360.13480.35480.12650.13790.66770.1730.656736.9696-13.880540.9629
52.8681-4.32591.57776.6952-1.96312.06960.32441.0480.2914-0.5191-0.5831-0.5413-0.10940.42780.27350.52320.03980.1120.59520.08770.391724.2257-5.738334.8543
68.48321.5753-4.85596.9926-2.91733.8579-0.0706-0.37070.41280.0776-0.2583-0.7268-0.59991.440.35380.352-0.0372-0.03280.4320.08470.485631.1085-5.73148.186
71.4662-1.29480.21394.6036-2.63333.79150.06930.17540.0356-0.1863-0.1254-0.06490.1060.11310.0620.23080.0120.00340.3063-0.00480.3415.84-11.042349.6116
84.2978-3.9244-1.49283.57210.90667.3579-0.4556-0.8502-0.34960.86470.0139-0.04130.17190.83660.39690.27140.00980.0520.44830.08150.386517.3553-18.062761.3132
90.6491.38220.86055.5946-1.23194.5905-0.42310.5952-0.1013-0.50990.1716-0.70510.19181.31840.25280.6835-0.04330.12020.9434-0.05350.431426.9255-0.40796.6387
101.48890.1702-0.35654.77281.46950.56150.0222-0.08440.11720.4601-0.1842-0.238-0.13650.23160.11540.61980.0382-0.03080.87420.04850.339724.3628-2.327316.4078
112.64991.0376-0.20185.8861.2675.25750.0291-0.3101-0.13760.9085-0.075-0.10540.50990.5962-0.01710.57510.0647-0.05780.69620.03360.409823.7998-12.650918.9876
128.59923.28372.58812.89561.15112.2645-0.0893-0.4708-1.33360.7718-0.2381-1.57911.39720.77030.16621.25770.4104-0.2510.90040.13391.066627.5306-28.645221.1202
135.2619-1.4688-1.08837.6966-0.61430.43140.2094-0.0475-0.43820.2936-0.2099-0.20860.47070.0430.04080.73650.0457-0.10810.71250.04540.403115.4918-20.401419.6545
141.04620.00841.17822.6475-0.43552.35160.27870.2754-0.214-0.5175-0.3993-0.27760.53250.65940.12650.7160.21390.01730.7573-0.00990.373324.7506-13.82217.9378
159.1044-3.3138-3.20863.28520.25881.5059-0.1069-0.64970.17820.43070.2356-0.18170.09180.6339-0.13180.64380.04770.01710.6615-0.04020.299513.3415-6.822912.5182
161.993-0.9233-1.75542.10580.89289.5396-0.10571.0806-0.3682-0.8457-0.4382-0.64321.16670.52780.48060.70270.18460.07060.72080.02410.460223.4791-8.97591.1796
177.15482.4255-1.81684.6083-2.16543.8616-0.0033-0.3267-0.57960.2879-0.09-0.00410.17650.33980.0880.31230.0402-0.00270.32540.07730.39197.8215-25.27974.5335
183.9630.9343-0.84892.8-0.43442.0523-0.0166-0.2791-0.2010.1419-0.0478-0.04180.1097-0.06740.04770.2997-0.0265-0.00710.27760.03830.3783-5.6206-23.821277.732
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 170 )
4X-RAY DIFFRACTION4chain 'A' and (resid 171 through 181 )
5X-RAY DIFFRACTION5chain 'A' and (resid 182 through 193 )
6X-RAY DIFFRACTION6chain 'A' and (resid 194 through 207 )
7X-RAY DIFFRACTION7chain 'A' and (resid 208 through 255 )
8X-RAY DIFFRACTION8chain 'A' and (resid 256 through 271 )
9X-RAY DIFFRACTION9chain 'B' and (resid 96 through 113 )
10X-RAY DIFFRACTION10chain 'B' and (resid 114 through 143 )
11X-RAY DIFFRACTION11chain 'B' and (resid 144 through 170 )
12X-RAY DIFFRACTION12chain 'B' and (resid 171 through 181 )
13X-RAY DIFFRACTION13chain 'B' and (resid 182 through 193 )
14X-RAY DIFFRACTION14chain 'B' and (resid 194 through 207 )
15X-RAY DIFFRACTION15chain 'B' and (resid 208 through 255 )
16X-RAY DIFFRACTION16chain 'B' and (resid 256 through 271 )
17X-RAY DIFFRACTION17chain 'C' and (resid 96 through 138 )
18X-RAY DIFFRACTION18chain 'C' and (resid 139 through 271 )

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