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- PDB-7zos: Class 1 Phytoglobin from Sugar beet (BvPgb1.2) -

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Basic information

Entry
Database: PDB / ID: 7zos
TitleClass 1 Phytoglobin from Sugar beet (BvPgb1.2)
ComponentsNon-symbiotic hemoglobin class 1
KeywordsOXYGEN BINDING / Plant Hemoglobin / Phytoglobin / Nitrogen Metabolism / Redox balance
Function / homology
Function and homology information


oxygen binding / heme binding / metal ion binding
Similarity search - Function
Leghaemoglobin / Globin/Protoglobin / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
CYANIDE ION / HEXACYANOFERRATE(3-) / PROTOPORPHYRIN IX CONTAINING FE / Non-symbiotic hemoglobin class 1
Similarity search - Component
Biological speciesBeta vulgaris (beet)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNyblom, M. / Christensen, S. / Eriksson, N. / Bulow, L.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council Sweden
The Swedish Foundation for Strategic Research Sweden
CitationJournal: Antioxidants / Year: 2022
Title: Oxidative Implications of Substituting a Conserved Cysteine Residue in Sugar Beet Phytoglobin BvPgb 1.2.
Authors: Christensen, S. / Groth, L. / Leiva-Eriksson, N. / Nyblom, M. / Bulow, L.
History
DepositionApr 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Advisory / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.2Feb 7, 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: Non-symbiotic hemoglobin class 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1084
Polymers19,2531
Non-polymers8543
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Gel filtration (Size Exclusion Chromatography) has been performed. This relieved a close to complete dimerization of the protein.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-22 kcal/mol
Surface area8170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.750, 96.750, 47.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

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Components

#1: Protein Non-symbiotic hemoglobin class 1 / BvPgb1.2


Mass: 19253.303 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Beta vulgaris (beet) / Gene: Bv9_224250_aayd.t2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: V5QR23
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#4: Chemical ChemComp-FC6 / HEXACYANOFERRATE(3-) / FERRI(III)HEXACYANIDE


Mass: 211.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6FeN6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.91 Å3/Da / Density % sol: 57.75 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG6000, 0.1 M Citrate, pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→68.413 Å / Num. obs: 18443 / % possible obs: 100 % / Redundancy: 25.6 % / Biso Wilson estimate: 38.56 Å2 / CC1/2: 0.999 / Net I/σ(I): 23.7
Reflection shellResolution: 1.901→1.934 Å / Num. unique obs: 907 / CC1/2: 0.727

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Processing

Software
NameVersionClassification
MxCuBEdata collection
autoPROCdata processing
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.14_3260refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3zhw

3zhw


Resolution: 1.9→47.9 Å / SU ML: 0.1629 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.2442 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2353 969 5.25 %
Rwork0.2027 17471 -
obs0.2038 18440 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.94 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1145 0 58 95 1298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01051232
X-RAY DIFFRACTIONf_angle_d1.46491669
X-RAY DIFFRACTIONf_chiral_restr0.0566178
X-RAY DIFFRACTIONf_plane_restr0.0065198
X-RAY DIFFRACTIONf_dihedral_angle_d5.9939716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-20.29221360.25632443X-RAY DIFFRACTION100
2-2.130.26681300.23062441X-RAY DIFFRACTION100
2.13-2.290.24511340.20932463X-RAY DIFFRACTION99.92
2.29-2.520.27961440.2122460X-RAY DIFFRACTION100
2.52-2.890.23271210.21122501X-RAY DIFFRACTION100
2.89-3.640.23341500.22272503X-RAY DIFFRACTION100
3.64-47.90.21971540.17972660X-RAY DIFFRACTION99.89

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