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- PDB-8qvb: Crystal structure of chlorite dismutase at 3000 eV based on a com... -

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Basic information

Entry
Database: PDB / ID: 8qvb
TitleCrystal structure of chlorite dismutase at 3000 eV based on a combination of spherical harmonics and analytical absorption corrections
ComponentsChlorite Dismutase
KeywordsOXIDOREDUCTASE / long-wavelength x-ray diffraction
Function / homologyhydrogen peroxide-dependent heme synthase / Heme-dependent peroxidase ChdC/CLD / Chlorite dismutase / Dimeric alpha-beta barrel / oxidoreductase activity / heme binding / metal ion binding / PROTOPORPHYRIN IX CONTAINING FE / hydrogen peroxide-dependent heme synthase
Function and homology information
Biological speciesCyanothece sp. PCC 7425 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDuman, R. / Wagner, A. / Kamps, J. / Orville, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Diamond Light Source United Kingdom
CitationJournal: J.Appl.Crystallogr. / Year: 2024
Title: Ray-tracing analytical absorption correction for X-ray crystallography based on tomographic reconstructions.
Authors: Lu, Y. / Duman, R. / Beilsten-Edmands, J. / Winter, G. / Basham, M. / Evans, G. / Kamps, J.J.A.G. / Orville, A.M. / Kwong, H.S. / Beis, K. / Armour, W. / Wagner, A.
History
DepositionOct 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chlorite Dismutase
B: Chlorite Dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,33810
Polymers43,6622
Non-polymers1,6768
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-74 kcal/mol
Surface area16270 Å2
Unit cell
Length a, b, c (Å)51.557, 52.755, 54.952
Angle α, β, γ (deg.)107.21, 99.03, 109.31
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Chlorite Dismutase


Mass: 21830.881 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanothece sp. PCC 7425 (bacteria) / Gene: Cyan7425_1434 / Production host: Escherichia coli (E. coli) / References: UniProt: B8HNS6

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Non-polymers , 5 types, 60 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 57.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 150mM MgSO4, 100mM MES, pH 6.5 and 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 4.132 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: May 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 4.132 Å / Relative weight: 1
ReflectionResolution: 2.7→50.35 Å / Num. obs: 13696 / % possible obs: 99.43 % / Redundancy: 41.1 % / CC1/2: 0.999 / Net I/σ(I): 44.73
Reflection shellResolution: 2.7→2.797 Å / Num. unique obs: 1351 / CC1/2: 0.993

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→50.35 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.916 / SU B: 8.916 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 1.473 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21841 688 5 %RANDOM
Rwork0.17162 ---
obs0.174 13042 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.439 Å2
Baniso -1Baniso -2Baniso -3
1-4.83 Å2-0.54 Å20.48 Å2
2---1.11 Å2-1.13 Å2
3----1.43 Å2
Refinement stepCycle: 1 / Resolution: 2.7→50.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3034 0 61 52 3147
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123209
X-RAY DIFFRACTIONr_bond_other_d0.0030.0163026
X-RAY DIFFRACTIONr_angle_refined_deg1.4461.6934376
X-RAY DIFFRACTIONr_angle_other_deg0.4951.6036899
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4975368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.534534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.64610538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0660.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023946
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02842
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.092.8231466
X-RAY DIFFRACTIONr_mcbond_other2.092.8231466
X-RAY DIFFRACTIONr_mcangle_it3.3215.0691836
X-RAY DIFFRACTIONr_mcangle_other3.3225.071837
X-RAY DIFFRACTIONr_scbond_it2.9793.0781743
X-RAY DIFFRACTIONr_scbond_other2.9783.0791744
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8075.5042541
X-RAY DIFFRACTIONr_long_range_B_refined6.19827.93497
X-RAY DIFFRACTIONr_long_range_B_other6.19727.943488
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.765 Å
RfactorNum. reflection% reflection
Rfree0.285 60 -
Rwork0.201 937 -
obs--94.23 %

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