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- PDB-8v2y: Room temperature X-ray Crystal Structure of FMN-bound long-chain ... -

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Basic information

Entry
Database: PDB / ID: 8v2y
TitleRoom temperature X-ray Crystal Structure of FMN-bound long-chain flavodoxin from Rhodopseudomonas palustris
ComponentsFlavodoxin
KeywordsFLAVOPROTEIN / FMN-bound long chain Flavodoxin
Function / homology
Function and homology information


FMN binding / electron transfer activity
Similarity search - Function
Flavodoxin, long chain / : / Flavodoxin, conserved site / Flavodoxin signature. / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Flavodoxin
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsAnsari, A. / Khan, S.A. / Miller, A.F.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0021283 United States
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structure, dynamics, and redox reactivity of an all-purpose flavodoxin.
Authors: Khan, S. / Ansari, A. / Brachi, M. / Das, D. / El Housseini, W. / Minteer, S. / Miller, A.F.
History
DepositionNov 24, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flavodoxin
B: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6824
Polymers35,7702
Non-polymers9132
Water1,54986
1
A: Flavodoxin
hetero molecules

B: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6824
Polymers35,7702
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area3050 Å2
ΔGint-18 kcal/mol
Surface area13700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.692, 58.878, 60.898
Angle α, β, γ (deg.)90.000, 105.470, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid -6 through 19 or (resid 20...
d_2ens_1(chain "B" and (resid -6 through 33 or (resid 34...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ALAALATYRTYRAA-6 - 531 - 60
d_12ASPASPGLYGLYAA57 - 8564 - 92
d_13THRTHRTYRTYRAA88 - 9095 - 97
d_14PHEPHEGLYGLYAA94 - 120101 - 127
d_15LYSLYSALAALAAA127 - 128134 - 135
d_16ASPASPTHRTHRAA131 - 160138 - 167
d_17FMNFMNFMNFMNAC201
d_21ALAALATHRTHRBB-6 - 1601 - 167
d_22FMNFMNFMNFMNBD201

NCS oper: (Code: givenMatrix: (-0.995035782273, 0.0075197324557, -0.0992332888701), (0.0366232366679, 0.954833993936, -0.294874180896), (0.0925339425948, -0.297044605484, -0.950369387039)Vector: 0. ...NCS oper: (Code: given
Matrix: (-0.995035782273, 0.0075197324557, -0.0992332888701), (0.0366232366679, 0.954833993936, -0.294874180896), (0.0925339425948, -0.297044605484, -0.950369387039)
Vector: 0.642816501744, -4.02474641622, -30.0266723298)

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Components

#1: Protein Flavodoxin


Mass: 17884.822 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Gene: RPA2117 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6N7Y7
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.26 Å3/Da / Density % sol: 45.46 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.3-0.6M magnesium formate, 15-20% polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5406 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Oct 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.86→28.27 Å / Num. obs: 7368 / % possible obs: 97.83 % / Redundancy: 3.6 % / Biso Wilson estimate: 47.92 Å2 / CC1/2: 0.922 / Rmerge(I) obs: 0.1291 / Rrim(I) all: 0.1528 / Net I/σ(I): 9.11
Reflection shellResolution: 2.86→3.08 Å / Num. unique obs: 1366 / CC1/2: 0.842

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Cootmodel building
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.86→28.27 Å / SU ML: 0.3659 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.1821
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2752 737 10.02 %
Rwork0.2193 6619 -
obs0.2249 7356 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.74 Å2
Refinement stepCycle: LAST / Resolution: 2.86→28.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2314 0 62 87 2463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00572409
X-RAY DIFFRACTIONf_angle_d0.78463269
X-RAY DIFFRACTIONf_chiral_restr0.0549380
X-RAY DIFFRACTIONf_plane_restr0.0036431
X-RAY DIFFRACTIONf_dihedral_angle_d15.0751840
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.735412693386 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.86-3.080.36131370.29191229X-RAY DIFFRACTION91.07
3.08-3.380.35181490.25131345X-RAY DIFFRACTION99.87
3.39-3.870.26851490.22261335X-RAY DIFFRACTION99.73
3.87-4.870.23161490.18031339X-RAY DIFFRACTION99.87
4.88-28.270.25841530.21451371X-RAY DIFFRACTION98.64

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