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- PDB-6xhh: Far-red absorbing dark state of JSC1_58120g3 with bound 18-1, 18-... -

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Basic information

Entry
Database: PDB / ID: 6xhh
TitleFar-red absorbing dark state of JSC1_58120g3 with bound 18-1, 18-2 dihydrobiliverdin IXa (DHBV), the native chromophore precursor
ComponentsJSC1_58120g3
KeywordsSIGNALING PROTEIN / Cyanobacteriochrome GAF Domain Phytochrome-superfamily 18-1 / 18-2 Dihydrobiliverdin
Function / homologymesobiliverdin IX(alpha)
Function and homology information
Biological species[Leptolyngbya] sp. JSC-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMoreno, M.V. / Rockwell, N.C. / Fisher, A.J. / Lagarias, J.C.
Funding support United States, 3items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FG02-09ER16117 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM068552 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32-GM07377 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: A far-red cyanobacteriochrome lineage specific for verdins.
Authors: Moreno, M.V. / Rockwell, N.C. / Mora, M. / Fisher, A.J. / Lagarias, J.C.
History
DepositionJun 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 18, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: JSC1_58120g3
B: JSC1_58120g3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,72312
Polymers42,0532
Non-polymers1,67010
Water6,774376
1
A: JSC1_58120g3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9247
Polymers21,0271
Non-polymers8976
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: JSC1_58120g3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8005
Polymers21,0271
Non-polymers7734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.286, 35.814, 74.875
Angle α, β, γ (deg.)100.190, 95.370, 89.860
Int Tables number1
Space group name H-MP1

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Components

#1: Protein JSC1_58120g3


Mass: 21026.643 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) [Leptolyngbya] sp. JSC-1 (bacteria) / Plasmid: pBAD-CBD
Details (production host): intein-CBD tag, Ampicillin resistance
Production host: Escherichia coli (E. coli) / Strain (production host): LMG 194
#2: Chemical ChemComp-M1V / mesobiliverdin IX(alpha)


Mass: 586.678 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H38N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Nonpolymer detailsThe added ligand was 18-1, 18-2 dihydrobiliverdin IXa that forms a covalent adduct with the ...The added ligand was 18-1, 18-2 dihydrobiliverdin IXa that forms a covalent adduct with the protein, which is equivalent to a mesobiliverdin IXa moiety bonded to Cys636.

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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: 2.02 Å3/Da / Density % sol: 39.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.25 M Ammonium Citrate, 25% (v/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→36.68 Å / Num. obs: 44374 / % possible obs: 84.3 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.031 / Rrim(I) all: 0.06 / Net I/σ(I): 13.8 / Num. measured all: 169907
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.8 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.5-1.530.57478512650.7970.3360.6622.248.9
8.22-36.680.02121231510.0120.02344.198.1

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Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
PHENIX1.14-3260-000refinement
PDB_EXTRACT3.25data extraction
Aimless0.7.1data reduction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W2Z

3w2z


Resolution: 1.5→30.521 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 26.47
RfactorNum. reflection% reflection
Rfree0.2313 2185 4.93 %
Rwork0.1944 --
obs0.1963 44337 84.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.58 Å2 / Biso mean: 20.7147 Å2 / Biso min: 7.44 Å2
Refinement stepCycle: final / Resolution: 1.5→30.521 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2932 0 118 378 3428
Biso mean--19.31 30.28 -
Num. residues----359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063125
X-RAY DIFFRACTIONf_angle_d1.0044221
X-RAY DIFFRACTIONf_dihedral_angle_d6.3962527
X-RAY DIFFRACTIONf_chiral_restr0.056430
X-RAY DIFFRACTIONf_plane_restr0.005546
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5-1.53270.2823880.2417155950
1.5327-1.56830.3243860.2468199563
1.5683-1.60750.2891290.2305258582
1.6075-1.6510.27291320.2205276090
1.651-1.69960.26271420.2215285090
1.6996-1.75440.22711430.2218270988
1.7544-1.81710.28631310.2194259383
1.8171-1.88990.2981420.2063281990
1.8899-1.97590.25451540.2054280690
1.9759-2.080.24591560.1977276288
2.08-2.21030.2321330.1883260283
2.2103-2.38090.21441460.1937286091
2.3809-2.62040.24181660.1983282091
2.6204-2.99930.24291440.1885274088
2.9993-3.77760.19641530.1741284992
3.7776-30.520.20071400.1828284390

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