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- PDB-8hgr: The apo-flavodoxin monomer from Synechococcus elongatus PCC 7942 -

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Basic information

Entry
Database: PDB / ID: 8hgr
TitleThe apo-flavodoxin monomer 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
Biological speciesSynechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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)20,8413
Polymers20,7821
Non-polymers602
Water2,450136
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-18 kcal/mol
Surface area7670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.281, 50.544, 69.325
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.12 Å3/Da / Density % sol: 41.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Magnesium chloride; 0.1 M Tris-HCl pH8.5; 30% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 15654 / % possible obs: 97.5 % / Redundancy: 11.6 % / Biso Wilson estimate: 23.79 Å2 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.03 / Net I/σ(I): 15.6
Reflection shellResolution: 1.84→1.93 Å / Rmerge(I) obs: 0.675 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1906 / Rpim(I) all: 0.298 / % possible all: 83.1

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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: 1.84→40.84 Å / SU ML: 0.1726 / Cross valid method: FREE R-VALUE / σ(F): 100 / Phase error: 19.2415
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.201 1498 9.96 %
Rwork0.162 13541 -
obs0.1659 15039 93.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.09 Å2
Refinement stepCycle: LAST / Resolution: 1.84→40.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1330 0 2 136 1468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00551360
X-RAY DIFFRACTIONf_angle_d0.77491847
X-RAY DIFFRACTIONf_chiral_restr0.0511198
X-RAY DIFFRACTIONf_plane_restr0.0059246
X-RAY DIFFRACTIONf_dihedral_angle_d17.6044481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.890.26721160.24051117X-RAY DIFFRACTION87.08
1.89-1.960.2714960.2257831X-RAY DIFFRACTION65.33
1.96-2.040.21511390.16261231X-RAY DIFFRACTION94.29
2.04-2.130.20651350.15681232X-RAY DIFFRACTION96.13
2.13-2.250.21331340.15851251X-RAY DIFFRACTION96.72
2.25-2.390.21251390.16261281X-RAY DIFFRACTION97.66
2.39-2.570.22971390.16371260X-RAY DIFFRACTION98.04
2.57-2.830.21121490.17081289X-RAY DIFFRACTION98.63
2.83-3.240.21191430.17021311X-RAY DIFFRACTION99.18
3.24-4.080.16041500.14111336X-RAY DIFFRACTION99.73
4.08-40.840.1941580.15711402X-RAY DIFFRACTION99.49

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