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- PDB-8hgq: The apo-flavodoxin dimer from Synechococcus elongatus PCC 7942 -

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Basic information

Entry
Database: PDB / ID: 8hgq
TitleThe apo-flavodoxin dimer from Synechococcus elongatus PCC 7942
ComponentsFlavodoxin
KeywordsELECTRON TRANSPORT / FLAVODOXIN / phosphate BINDING / REDOX POTENTIAL / FMN BINDING
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
PHOSPHATE ION / Flavodoxin
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsLiu, S.W. / Chen, Y.Y. / Gong, Y. / Cao, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32070259 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: A dimer-monomer transition captured by the crystal structures of cyanobacterial apo flavodoxin.
Authors: Liu, S. / Chen, Y. / Du, T. / Zhao, W. / Liu, X. / Zhang, H. / Yuan, Q. / Gao, L. / Dong, Y. / Gao, X. / Gong, Y. / Cao, P.
History
DepositionNov 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8772
Polymers20,7821
Non-polymers951
Water1,802100
1
A: Flavodoxin
hetero molecules

A: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7534
Polymers41,5632
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)49.560, 49.560, 161.025
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-977-

HOH

21A-978-

HOH

31A-998-

HOH

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Components

#1: Protein Flavodoxin


Mass: 20781.623 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Strain: PCC 7942 / FACHB-805 / Gene: isiB, Synpcc7942_1541 / Production host: Escherichia coli (E. coli) / References: UniProt: P10340
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.4 M NaH2PO4/1.6 M K2HPO4; 0.1 M imidazole PH8.0; 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 12295 / % possible obs: 96.6 % / Redundancy: 16.2 % / Biso Wilson estimate: 35.22 Å2 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.022 / Net I/σ(I): 20
Reflection shellResolution: 2.09→2.2 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1772 / Rpim(I) all: 0.189 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CZN

1czn


Resolution: 2.09→27 Å / SU ML: 0.2569 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.2208
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2394 599 4.94 %
Rwork0.1918 11533 -
obs0.1941 12132 95.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.62 Å2
Refinement stepCycle: LAST / Resolution: 2.09→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1334 0 5 100 1439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00651364
X-RAY DIFFRACTIONf_angle_d0.76421851
X-RAY DIFFRACTIONf_chiral_restr0.0494197
X-RAY DIFFRACTIONf_plane_restr0.0041246
X-RAY DIFFRACTIONf_dihedral_angle_d17.6654479
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.30.28281650.23872655X-RAY DIFFRACTION92.01
2.3-2.630.27581360.21962963X-RAY DIFFRACTION99.71
2.63-3.310.29241500.21642734X-RAY DIFFRACTION91.58
3.32-270.20081480.16733181X-RAY DIFFRACTION99.82
Refinement TLS params.Method: refined / Origin x: -5.13242171528 Å / Origin y: -18.9933120858 Å / Origin z: -9.17377621701 Å
111213212223313233
T0.154106702408 Å20.00695836143906 Å2-0.000400003516644 Å2-0.199872079914 Å2-0.0186595614323 Å2--0.176581680154 Å2
L0.887688804391 °20.1535243323 °2-0.196898454486 °2-0.806613676762 °2-0.273550655119 °2--0.912683504105 °2
S-0.0284746490107 Å °-0.00657407252455 Å °-0.0444361897258 Å °-0.0242941539371 Å °0.00182312875656 Å °0.0165239983032 Å °0.0742623801419 Å °0.0301335472227 Å °-2.6629190761E-9 Å °
Refinement TLS groupSelection details: all

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