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- PDB-6xhg: Far-red absorbing dark state of JSC1_58120g3 with bound biliverdi... -

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Basic information

Entry
Database: PDB / ID: 6xhg
TitleFar-red absorbing dark state of JSC1_58120g3 with bound biliverdin IXa (BV)
ComponentsJSC1_58120g3
KeywordsSIGNALING PROTEIN / Cyanobacteriochrome GAF Domain Phytochrome superfamily Biliverdin
Function / homologyChem-BVX
Function and homology information
Biological species[Leptolyngbya] sp. JSC-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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 1.3Apr 3, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)43,2855
Polymers42,0532
Non-polymers1,2313
Water1,17165
1
A: JSC1_58120g3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6733
Polymers21,0271
Non-polymers6472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: JSC1_58120g3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6112
Polymers21,0271
Non-polymers5851
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.220, 36.130, 75.490
Angle α, β, γ (deg.)100.540, 95.550, 90.010
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 523 through 699 or resid 801))
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: TYR / End label comp-ID: TYR / Auth seq-ID: 523 - 699 / Label seq-ID: 3 - 179

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and (resid 523 through 699 or resid 801))AA
2chain BBB

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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-BVX / 3-[2-[(~{Z})-[5-[(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-pyrrol-2-ylidene]methyl]-5-[(~{Z})-(3-ethyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid / Biliverdine IX alpha, bound form


Mass: 584.662 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H36N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.04 Å3/Da / Density % sol: 39.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Ammonium Chloride, 35% (w/v) PEG 6000, 0.1 M Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→73.86 Å / Num. obs: 12858 / % possible obs: 86.8 % / Redundancy: 1.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.074 / Rrim(I) all: 0.105 / Net I/σ(I): 2.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.3-2.381.70.39412960.7190.3940.55791.6
8.91-73.861.80.032210.9950.030.04286.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.89 Å36.93 Å
Translation3.89 Å36.93 Å

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
PHASER2.8.2phasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
Aimless0.7.3data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: JSC1_58120g3 with 18-1,18-2 DHBV-adduct

Resolution: 2.3→36.928 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 33.09
RfactorNum. reflection% reflection
Rfree0.2644 638 4.86 %
Rwork0.231 --
obs0.2326 12858 88.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 124.09 Å2 / Biso mean: 44.266 Å2 / Biso min: 11.93 Å2
Refinement stepCycle: final / Resolution: 2.3→36.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2890 0 90 65 3045
Biso mean--34.59 37.96 -
Num. residues----354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033051
X-RAY DIFFRACTIONf_angle_d0.7844134
X-RAY DIFFRACTIONf_dihedral_angle_d13.5841769
X-RAY DIFFRACTIONf_chiral_restr0.048422
X-RAY DIFFRACTIONf_plane_restr0.004536
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1748X-RAY DIFFRACTION4.795TORSIONAL
12B1748X-RAY DIFFRACTION4.795TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3001-2.47770.39651130.305255390
2.4777-2.72690.33951050.2823260692
2.7269-3.12130.32211430.2505236685
3.1213-3.93180.27281490.2146244187
3.9318-36.9280.19911280.2054252590
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)
13.6522-1.90790.7176.6224-3.77588.72110.48620.40140.3282-1.7558-1.2224-0.59620.7963-0.38040.52830.65690.14330.12020.6375-0.18560.6892-7.2347-9.32645.286
24.67991.755-2.27665.829-1.40016.7723-0.17620.6526-0.2801-0.3060.4466-0.24790.4357-0.1396-0.27580.2067-0.0029-0.04850.3107-0.03480.3892-17.0419-2.80058.8452
32.934-1.6917-0.07235.1025-1.39833.5993-0.0479-0.10060.09390.20.01780.2294-0.4964-0.29280.05460.2692-0.02650.09240.2549-0.02150.3097-18.71358.169619.5227
48.4912-0.4331-1.55812.3760.76293.651-0.2196-0.59650.24570.18050.0564-0.25740.27310.28490.16120.3953-0.02350.0190.3488-0.00590.2951-13.2432-5.249931.9167
54.2117-0.50843.07815.204-4.40045.7725-0.2909-1.67940.2160.68110.897-0.0019-0.1909-0.7365-0.41950.47270.01430.06350.4667-0.02860.2122-20.85481.08735.5157
61.2282-0.3266-0.59693.2360.91453.8423-0.0426-0.06150.11980.3029-0.00340.2749-0.0755-0.21390.06040.20890.02860.0040.23130.02290.2349-18.89620.443621.1365
77.75242.5398-2.18114.987-3.18965.1622-0.10040.47050.3690.82920.0187-0.4775-0.60580.07620.10330.3092-0.00690.00280.3438-0.02280.2799-6.5107-0.9913.4209
89.55565.04933.30983.35892.34289.9770.6972-1.00770.58540.8384-0.45880.55630.7609-0.3517-0.29380.73580.03650.18860.63090.28040.8137-27.5898-26.3923-0.9214
92.675-2.5076-2.13648.25041.37122.55620.1771-0.9730.07071.16670.3369-0.33940.6880.274-0.71230.46730.0448-0.03760.47980.00790.3677-19.2592-21.0616-2.3276
103.84470.76990.79624.31-0.07335.034-0.0229-0.34210.23010.3441-0.0282-0.1758-0.36750.09540.09340.3637-0.02350.05290.224-0.00790.3506-15.75-13.8183-11.5522
113.3381-0.6688-0.2134.3357-0.67843.99410.17090.4584-0.3497-0.17410.0316-0.318-0.54240.7894-0.13540.3419-0.03270.02280.3025-0.06120.3873-15.8695-9.733-18.4798
124.50050.1325-0.49072.92321.72845.63210.24930.9771-0.6129-0.348-0.2748-0.0640.2472-0.53820.08020.34370.0193-0.00690.3564-0.03890.3297-22.2589-22.2963-28.6663
130.3390.3191-0.34722.49290.66654.3086-0.04770.1536-0.0568-0.08990.1467-0.247-0.21790.5326-0.12570.2196-0.0374-0.0090.29580.00770.3509-15.7219-17.0101-19.1578
146.9308-2.2183-2.69739.48346.87579.69480.4230.15030.5054-0.1811-0.68790.1634-0.156-0.69650.29360.2714-0-0.02550.43020.02230.3131-28.668-18.918-9.9782
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 523:534)A523 - 534
2X-RAY DIFFRACTION2(chain A and resid 535:562)A535 - 562
3X-RAY DIFFRACTION3(chain A and resid 563:605)A563 - 605
4X-RAY DIFFRACTION4(chain A and resid 606:628)A606 - 628
5X-RAY DIFFRACTION5(chain A and resid 629:636)A629 - 636
6X-RAY DIFFRACTION6(chain A and resid 637:675)A637 - 675
7X-RAY DIFFRACTION7(chain A and resid 676:699)A676 - 699
8X-RAY DIFFRACTION8(chain B and resid 523:536)B523 - 536
9X-RAY DIFFRACTION9(chain B and resid 537:551)B537 - 551
10X-RAY DIFFRACTION10(chain B and resid 552:577)B552 - 577
11X-RAY DIFFRACTION11(chain B and resid 578:603)B578 - 603
12X-RAY DIFFRACTION12(chain B and resid 604:631)B604 - 631
13X-RAY DIFFRACTION13(chain B and resid 632:675)B632 - 675
14X-RAY DIFFRACTION14(chain B and resid 676:699)B676 - 699

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