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- PDB-6uyk: Dark-operative protochlorophyllide oxidoreductase in the nucleoti... -

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Basic information

Entry
Database: PDB / ID: 6uyk
TitleDark-operative protochlorophyllide oxidoreductase in the nucleotide-free form.
ComponentsLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein
KeywordsOXIDOREDUCTASE / Electron Transfer / Nitrogenase / DPOR / Photosynthesis / Iron-Sulfur cluster
Function / homology
Function and homology information


ferredoxin:protochlorophyllide reductase (ATP-dependent) / photosynthesis, dark reaction / light-independent bacteriochlorophyll biosynthetic process / oxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor / oxidoreductase activity, acting on iron-sulfur proteins as donors / 4 iron, 4 sulfur cluster binding / ATP binding / metal ion binding
Similarity search - Function
Light-independent protochlorophyllide reductase, iron-sulphur ATP-binding protein / NifH/frxC family / NifH/chlL conserved site / 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family / NifH/frxC family signature 2. / NifH/frxC family signature 1. / NIFH_FRXC family profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBacik, J.P. / Imran, S.M.S. / Watkins, M.B. / Corless, E. / Antony, E. / Ando, N.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0017866 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: The flexible N-terminus of BchL autoinhibits activity through interaction with its [4Fe-4S] cluster and released upon ATP binding.
Authors: Corless, E.I. / Saad Imran, S.M. / Watkins, M.B. / Bacik, J.P. / Mattice, J.R. / Patterson, A. / Danyal, K. / Soffe, M. / Kitelinger, R. / Seefeldt, L.C. / Origanti, S. / Bennett, B. / ...Authors: Corless, E.I. / Saad Imran, S.M. / Watkins, M.B. / Bacik, J.P. / Mattice, J.R. / Patterson, A. / Danyal, K. / Soffe, M. / Kitelinger, R. / Seefeldt, L.C. / Origanti, S. / Bennett, B. / Bothner, B. / Ando, N. / Antony, E.
History
DepositionNov 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.3Oct 11, 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: Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein
B: Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein
C: Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein
D: Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,1768
Polymers139,4014
Non-polymers7744
Water181
1
A: Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein
B: Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0884
Polymers69,7012
Non-polymers3872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-39 kcal/mol
Surface area20600 Å2
MethodPISA
2
C: Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein
D: Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0884
Polymers69,7012
Non-polymers3872
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-49 kcal/mol
Surface area20620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.513, 100.918, 117.789
Angle α, β, γ (deg.)90.000, 99.270, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

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Components

#1: Protein
Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / LI-POR subunit L


Mass: 34850.340 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: bchL, RHOS4_18930, RSP_0288 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9RFD6, ferredoxin:protochlorophyllide reductase (ATP-dependent)
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 1.95 Å3/Da / Density % sol: 36.81 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop
Details: 1 ul BchL protein in 100 mM HEPES pH 7.5, 150 mM NaCl, 10% (v/v) glycerol was mixed with 2 ul well solution containing 0.6 M sodium chloride, 0.1 M MES:NaOH pH 6.5, 20% (w/v) PEG 4000. Prior ...Details: 1 ul BchL protein in 100 mM HEPES pH 7.5, 150 mM NaCl, 10% (v/v) glycerol was mixed with 2 ul well solution containing 0.6 M sodium chloride, 0.1 M MES:NaOH pH 6.5, 20% (w/v) PEG 4000. Prior to freezing, the well solution was mixed in an equal volume of cryoprotectant solution with a final concentration of 9% (w/v) sucrose, 2% (w/v) glucose, 8% (v/v) glycerol, and 8% (v/v) ethylene glycol. Crystals were soaked for a few seconds in the cryoprotectant before being frozen in liquid nitrogen

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 1.008 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.6→42.2 Å / Num. obs: 32733 / % possible obs: 99.5 % / Redundancy: 9.3 % / Biso Wilson estimate: 80.66 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.057 / Net I/σ(I): 9.2
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.908 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3125 / CC1/2: 0.573 / Rpim(I) all: 0.413 / % possible all: 95.3

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FWY

3fwy


Resolution: 2.6→41.71 Å / SU ML: 0.4791 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.6425
RfactorNum. reflection% reflection
Rfree0.2772 2873 8.78 %
Rwork0.2314 --
obs0.2354 32732 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 85.6 Å2
Refinement stepCycle: LAST / Resolution: 2.6→41.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7648 0 18 1 7667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00197814
X-RAY DIFFRACTIONf_angle_d0.39310651
X-RAY DIFFRACTIONf_chiral_restr0.03981255
X-RAY DIFFRACTIONf_plane_restr0.00341396
X-RAY DIFFRACTIONf_dihedral_angle_d14.00582690
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.640.44751290.35511325X-RAY DIFFRACTION91.1
2.64-2.690.38341310.34521356X-RAY DIFFRACTION97.19
2.69-2.740.41921360.33541418X-RAY DIFFRACTION99.49
2.74-2.790.3721360.32111417X-RAY DIFFRACTION100
2.79-2.850.33841250.31441436X-RAY DIFFRACTION100
2.85-2.910.34091250.30651414X-RAY DIFFRACTION100
2.91-2.980.34151470.29791449X-RAY DIFFRACTION100
2.98-3.050.3581340.29571425X-RAY DIFFRACTION100
3.05-3.130.40471340.30861414X-RAY DIFFRACTION100
3.13-3.230.36431400.291398X-RAY DIFFRACTION100
3.23-3.330.31431410.28731433X-RAY DIFFRACTION100
3.33-3.450.3451420.26451428X-RAY DIFFRACTION100
3.45-3.590.34771360.24641432X-RAY DIFFRACTION100
3.59-3.750.31461380.25331410X-RAY DIFFRACTION100
3.75-3.950.28421430.24331432X-RAY DIFFRACTION100
3.95-4.20.27881360.22261436X-RAY DIFFRACTION100
4.2-4.520.25121400.20551450X-RAY DIFFRACTION100
4.52-4.970.24211380.19941413X-RAY DIFFRACTION100
4.97-5.690.27261400.21171457X-RAY DIFFRACTION100
5.69-7.160.26481390.22661440X-RAY DIFFRACTION100
7.16-41.710.18931430.17911476X-RAY DIFFRACTION99.94

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