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- PDB-5mg0: Structure of PAS-GAF fragment of Deinococcus phytochrome by seria... -

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Basic information

Entry
Database: PDB / ID: 5mg0
TitleStructure of PAS-GAF fragment of Deinococcus phytochrome by serial femtosecond crystallography
ComponentsBacteriophytochrome
KeywordsTRANSFERASE / phytochrome / photoreceptor / bilin / sfx
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 / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / GAF domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / PAS domain ...Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / GAF domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / PAS domain / Signal transduction histidine kinase-related protein, C-terminal / 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 / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-LBV / NICKEL (II) ION / Bacteriophytochrome
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsBurgie, E.S. / Fuller, F.D. / Gul, S. / Miller, M.D. / Young, I.D. / Brewster, A.S. / Clinger, J. / Aller, P. / Braeuer, P. / Hutchison, C. ...Burgie, E.S. / Fuller, F.D. / Gul, S. / Miller, M.D. / Young, I.D. / Brewster, A.S. / Clinger, J. / Aller, P. / Braeuer, P. / Hutchison, C. / Alonso-Mori, R. / Kern, J. / Yachandra, V.K. / Yano, J. / Sauter, N.K. / Phillips Jr., G.N. / Vierstra, R.D. / Orville, A.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science FoundationMCB-1329956 United States
CitationJournal: Nat. Methods / Year: 2017
Title: Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers.
Authors: Fuller, F.D. / Gul, S. / Chatterjee, R. / Burgie, E.S. / Young, I.D. / Lebrette, H. / Srinivas, V. / Brewster, A.S. / Michels-Clark, T. / Clinger, J.A. / Andi, B. / Ibrahim, M. / Pastor, E. ...Authors: Fuller, F.D. / Gul, S. / Chatterjee, R. / Burgie, E.S. / Young, I.D. / Lebrette, H. / Srinivas, V. / Brewster, A.S. / Michels-Clark, T. / Clinger, J.A. / Andi, B. / Ibrahim, M. / Pastor, E. / de Lichtenberg, C. / Hussein, R. / Pollock, C.J. / Zhang, M. / Stan, C.A. / Kroll, T. / Fransson, T. / Weninger, C. / Kubin, M. / Aller, P. / Lassalle, L. / Brauer, P. / Miller, M.D. / Amin, M. / Koroidov, S. / Roessler, C.G. / Allaire, M. / Sierra, R.G. / Docker, P.T. / Glownia, J.M. / Nelson, S. / Koglin, J.E. / Zhu, D. / Chollet, M. / Song, S. / Lemke, H. / Liang, M. / Sokaras, D. / Alonso-Mori, R. / Zouni, A. / Messinger, J. / Bergmann, U. / Boal, A.K. / Bollinger, J.M. / Krebs, C. / Hogbom, M. / Phillips, G.N. / Vierstra, R.D. / Sauter, N.K. / Orville, A.M. / Kern, J. / Yachandra, V.K. / Yano, J.
History
DepositionNov 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references
Revision 1.2Apr 12, 2017Group: Database references
Revision 1.3Nov 29, 2017Group: Database references / Category: pdbx_database_related
Revision 1.4Nov 14, 2018Group: Data collection / Source and taxonomy / Category: diffrn / entity_src_gen
Item: _diffrn.pdbx_serial_crystal_experiment / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.5Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8026
Polymers37,0241
Non-polymers7775
Water2,864159
1
A: Bacteriophytochrome
hetero molecules

A: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,60312
Polymers74,0492
Non-polymers1,55510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area6460 Å2
ΔGint-78 kcal/mol
Surface area27200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.535, 53.385, 80.912
Angle α, β, γ (deg.)90.000, 116.320, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Bacteriophytochrome / Phytochrome-like protein


Mass: 37024.250 Da / Num. of mol.: 1 / Mutation: Y307S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: bphP, DR_A0050 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9RZA4, histidine kinase

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Non-polymers , 5 types, 164 molecules

#2: 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
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.37 Å3/Da / Density % sol: 48.03 % / Description: ~50 micron crystalline plates
Crystal growTemperature: 298 K / Method: batch mode / pH: 5.6 / Details: PEG 3350, isopropanol, glycerol, sodium citrate / Temp details: room temperature

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Data collection

DiffractionMean temperature: 298 K / Ambient temp details: room temperature / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.265 Å
DetectorType: RAYONIX MX170-HS / Detector: CCD / Date: Sep 30, 2016 / Details: Compound refractive lenses
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.265 Å / Relative weight: 1
ReflectionResolution: 1.65→72.5 Å / Num. obs: 41877 / % possible obs: 99.97 % / Redundancy: 72.62 % / CC1/2: 0.968 / Net I/σ(I): 62.83
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsCC1/2Diffraction-ID% possible all
3.5548-72.5237195.78371.6770.95199.81
2.8215-3.5548129.9116.9220.9391100
2.4648-2.8215101.250.6680.8911100
2.2394-2.464876.6930.1560.8691100
2.0789-2.239458.9718.7280.7941100
1.9563-2.078946.2211.7850.7711100
1.8583-1.956338.257.4340.6641100
1.7774-1.858331.514.890.4341100
1.709-1.777425.213.4980.191100
1.65-1.70917.052.4140.087199.93

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.54 Å32.24 Å
Translation6.54 Å32.24 Å

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Processing

Software
NameVersionClassification
cctbx.xfeldata collection
cctbx.primedata reduction
cctbx.xfeldata reduction
PHASER2.6.0phasing
PHENIXrefinement
Cootmodel building
PDB_EXTRACT3.2data extraction
psanadata reduction
cctbx.primedata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 2O9C lacking the bilin and all neighboring side chains

2o9c


Resolution: 1.65→32.243 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.3
RfactorNum. reflection% reflection
Rfree0.2026 1925 4.61 %
Rwork0.1723 --
obs0.1737 41718 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 135.18 Å2 / Biso mean: 42.0992 Å2 / Biso min: 19.18 Å2
Refinement stepCycle: final / Resolution: 1.65→32.243 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2468 0 50 160 2678
Biso mean--34.39 48.24 -
Num. residues----322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062724
X-RAY DIFFRACTIONf_angle_d0.9543744
X-RAY DIFFRACTIONf_chiral_restr0.054420
X-RAY DIFFRACTIONf_plane_restr0.006492
X-RAY DIFFRACTIONf_dihedral_angle_d20.9091648
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.69130.44041370.39422786292398
1.6913-1.7370.35121390.334227872926100
1.737-1.78810.33711220.286228232945100
1.7881-1.84580.29371490.257528513000100
1.8458-1.91180.28491390.234828102949100
1.9118-1.98830.26721390.211928302969100
1.9883-2.07880.23631230.198928462969100
2.0788-2.18840.22411500.181128563006100
2.1884-2.32540.21261220.180728312953100
2.3254-2.50490.21331530.186128513004100
2.5049-2.75690.26661320.184228472979100
2.7569-3.15550.19711370.175828442981100
3.1555-3.97440.15681420.142428833025100
3.9744-32.24940.1621410.134429483089100
Refinement TLS params.Method: refined / Origin x: 100.9954 Å / Origin y: 1.9081 Å / Origin z: 14.029 Å
111213212223313233
T0.1887 Å2-0.0227 Å2-0.0087 Å2-0.2497 Å20.0203 Å2--0.2363 Å2
L1.1604 °2-0.3475 °2-0.1544 °2-0.9966 °20.5285 °2--1.8662 °2
S0.0165 Å °-0.0612 Å °0.0122 Å °0.044 Å °-0.0187 Å °0.0417 Å °-0.0504 Å °0.0012 Å °0.0036 Å °
Refinement TLS groupSelection details: chain 'A' and (resid 4 through 550 )

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