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- PDB-7ylr: Structure of a bacteria protein -

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Basic information

Entry
Database: PDB / ID: 7ylr
TitleStructure of a bacteria protein
ComponentsFerredoxin
KeywordsMETAL BINDING PROTEIN / a bacteria protein / FLAVOPROTEIN
Function / homology
Function and homology information


2 iron, 2 sulfur cluster binding / oxidoreductase activity / nucleotide binding / metal ion binding
Similarity search - Function
: / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily ...: / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Ferredoxin
Similarity search - Component
Biological speciesVariovorax paradoxus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsZhang, H. / Ma, Y.J. / Yu, G.M. / Li, X.Z.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
CitationJournal: To Be Published
Title: Structure of a bacteria protein
Authors: Zhang, H. / Ma, Y.J. / Yu, G.M. / Li, X.Z.
History
DepositionJul 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: 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: Ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3933
Polymers35,7611
Non-polymers6322
Water7,206400
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-24 kcal/mol
Surface area14950 Å2
Unit cell
Length a, b, c (Å)47.217, 84.042, 87.864
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 Ferredoxin


Mass: 35760.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Variovorax paradoxus (bacteria) / Gene: Vapar_1492 / Production host: Escherichia coli (E. coli) / References: UniProt: C5CSP5
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 2.44 Å3/Da / Density % sol: 49.54 %
Crystal growTemperature: 291.15 K / Method: liquid diffusion
Details: BIS-TRIS propane, Sodium malonate, Calcium chloride dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.68→60.73 Å / Num. obs: 37364 / % possible obs: 91.8 % / Redundancy: 11.1 % / Biso Wilson estimate: 20.24 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.4
Reflection shellResolution: 1.68→1.74 Å / Num. unique obs: 2363 / CC1/2: 0.894

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIX1.20_4459phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold2

Resolution: 1.68→41.59 Å / SU ML: 0.1254 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.2169
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2095 1835 4.91 %
Rwork0.1774 35518 -
obs0.179 37353 91.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.58 Å2
Refinement stepCycle: LAST / Resolution: 1.68→41.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2467 0 35 400 2902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00672550
X-RAY DIFFRACTIONf_angle_d0.96713460
X-RAY DIFFRACTIONf_chiral_restr0.0581381
X-RAY DIFFRACTIONf_plane_restr0.0096461
X-RAY DIFFRACTIONf_dihedral_angle_d12.9575369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.720.2005920.19941664X-RAY DIFFRACTION57.18
1.72-1.770.23811040.19781985X-RAY DIFFRACTION67.98
1.77-1.830.26081220.20812385X-RAY DIFFRACTION79.99
1.83-1.90.21851070.21012671X-RAY DIFFRACTION89.73
1.9-1.970.24771340.18522853X-RAY DIFFRACTION97.2
1.97-2.060.21561560.19322937X-RAY DIFFRACTION99.87
2.06-2.170.21421550.18162966X-RAY DIFFRACTION99.81
2.17-2.310.21761890.1882898X-RAY DIFFRACTION99.84
2.31-2.490.25771530.19093002X-RAY DIFFRACTION99.84
2.49-2.740.22011520.18792954X-RAY DIFFRACTION99.9
2.74-3.130.19411410.18573024X-RAY DIFFRACTION99.69
3.13-3.940.19381680.15823023X-RAY DIFFRACTION99.75
3.95-41.590.18871620.15883156X-RAY DIFFRACTION99.4

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