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- PDB-4q0i: Deinococcus radiodurans BphP PAS-GAF D207A mutant -

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Basic information

Entry
Database: PDB / ID: 4q0i
TitleDeinococcus radiodurans BphP PAS-GAF D207A mutant
ComponentsBacteriophytochrome
KeywordsTRANSFERASE / PAS GAF / photosensor / response regulator
Function / homology
Function and homology information


osmosensory signaling via phosphorelay pathway / detection of visible light / phosphorelay response regulator activity / protein kinase activator activity / histidine kinase / phosphorelay sensor kinase activity / photoreceptor activity / regulation of DNA-templated transcription / ATP binding / identical protein binding
Similarity search - Function
: / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / GAF domain / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / PAS domain ...: / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / GAF domain / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / PAS domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / PAS domain superfamily / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Chem-LBV / Bacteriophytochrome
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.744 Å
AuthorsBurgie, E.S. / Vierstra, R.D.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Crystallographic and Electron Microscopic Analyses of a Bacterial Phytochrome Reveal Local and Global Rearrangements during Photoconversion.
Authors: Burgie, E.S. / Wang, T. / Bussell, A.N. / Walker, J.M. / Li, H. / Vierstra, R.D.
History
DepositionApr 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6864
Polymers36,9801
Non-polymers7063
Water4,864270
1
A: Bacteriophytochrome
hetero molecules

A: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3728
Polymers73,9602
Non-polymers1,4126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5530 Å2
ΔGint-34 kcal/mol
Surface area26260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.497, 51.327, 80.368
Angle α, β, γ (deg.)90.00, 115.75, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-634-

HOH

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Components

#1: Protein Bacteriophytochrome / Phytochrome-like protein


Mass: 36980.238 Da / Num. of mol.: 1 / Fragment: PAS-GAF / Mutation: D207A, Y307S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: bphP, DR_A0050 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RZA4, histidine kinase
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Chemical ChemComp-LBV / 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid / 2(R),3(E)- PHYTOCHROMOBILIN


Mass: 585.670 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H37N4O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 19% isopropano, 19% PEG 3350, 5% glycerol, 100 mM Citric acid(NaOH) pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 11, 2011
RadiationMonochromator: horizontal focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.744→36.5 Å / Num. all: 32752 / Num. obs: 32523 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.744→36.193 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 20.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1951 1649 5.07 %random
Rwork0.1612 ---
all0.163 32899 --
obs0.163 32498 98.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.744→36.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2397 0 51 270 2718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152765
X-RAY DIFFRACTIONf_angle_d1.6233818
X-RAY DIFFRACTIONf_dihedral_angle_d17.1811046
X-RAY DIFFRACTIONf_chiral_restr0.085424
X-RAY DIFFRACTIONf_plane_restr0.01509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.744-1.79530.18611190.20382458X-RAY DIFFRACTION95
1.7953-1.85320.24391340.22546X-RAY DIFFRACTION99
1.8532-1.91950.23171260.19052582X-RAY DIFFRACTION99
1.9195-1.99630.23151450.18152549X-RAY DIFFRACTION99
1.9963-2.08720.21721210.1662568X-RAY DIFFRACTION99
2.0872-2.19720.23521430.17012579X-RAY DIFFRACTION99
2.1972-2.33480.20161360.16232572X-RAY DIFFRACTION99
2.3348-2.51510.17961420.17362591X-RAY DIFFRACTION100
2.5151-2.76810.20561440.17112578X-RAY DIFFRACTION100
2.7681-3.16840.22451510.16582599X-RAY DIFFRACTION100
3.1684-3.99110.1741370.14692611X-RAY DIFFRACTION100
3.9911-36.20050.16991510.14372616X-RAY DIFFRACTION98
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)
19.453-2.9773-2.74376.57091.64193.47750.1326-0.4157-0.57130.5141-0.2505-0.3870.52740.46570.08660.4165-0.074-0.07320.38970.10610.224216.5492-31.515331.1317
24.9419-0.4399-0.03512.05251.4563.46210.0568-0.26820.7064-0.1344-0.22230.198-0.4328-0.50620.15410.26270.0422-0.00760.2847-0.06770.2829-0.7551-11.400921.9866
30.9396-0.8744-0.88152.78823.82095.90610.04590.10620.0981-0.4462-0.09990.0915-0.6225-0.12020.11480.20820.0037-0.03320.25030.02910.28893.9013-22.40934.0651
41.4704-0.02730.13841.70461.12562.46110.0229-0.1187-0.06290.16060.0188-0.12930.12010.143-0.02320.10990.0009-0.02340.12780.02760.154816.4974-27.247512.1146
54.91681.75731.34122.20063.38496.1714-0.07830.1391-0.48970.29050.3060.05170.31720.1591-0.21610.11110.0001-0.00810.2420.01920.17725.2146-32.86892.2105
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 118 )
3X-RAY DIFFRACTION3chain 'A' and (resid 119 through 152 )
4X-RAY DIFFRACTION4chain 'A' and (resid 153 through 298 )
5X-RAY DIFFRACTION5chain 'A' and (resid 299 through 324 )

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