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- PDB-7adf: SFX structure of dehaloperoxidase B in the ferric form -

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Basic information

Entry
Database: PDB / ID: 7adf
TitleSFX structure of dehaloperoxidase B in the ferric form
ComponentsDehaloperoxidase B
KeywordsOXIDOREDUCTASE / SFX / ferric / dehaloperoxidase / peroxidase / fixed-target
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / peroxidase activity / heme binding / metal ion binding
Similarity search - Function
Myoglobin-like, M family globin domain / Globin/Protoglobin / Globin / Globin / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMoreno Chicano, T. / Ebrahim, A.E. / Axford, D.A. / Sherrell, D.A. / Sugimoto, H. / Tono, K. / Owada, S. / Worrall, J.W. / Strange, R.W. / Owen, R.L. / Hough, M.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R021015/1 United Kingdom
CitationJournal: to be published
Title: SFX structure of dehaloperoxidase B in the ferric form
Authors: Moreno Chicano, T. / Carey, L.M. / Ebrahim, A.E. / Axford, D.A. / Beale, J.H. / Sherrell, D.A. / Sugimoto, H. / Tono, K. / Owada, S. / Worrall, J.W. / Strange, R.W. / Owen, R.L. / Hough, M.A.
History
DepositionSep 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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: Dehaloperoxidase B
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5166
Polymers31,0912
Non-polymers1,4254
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-57 kcal/mol
Surface area12710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.320, 67.910, 68.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dehaloperoxidase B


Mass: 15545.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amphitrite ornata (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NAV7
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.3 Å3/Da / Density % sol: 47 % / Description: Microcrystals
Crystal growTemperature: 278 K / Method: batch mode / pH: 6
Details: Batch microcrystallization was used, mixing 30 mg/ml DHP in 20 mM MES pH 6.0 with 40%(w/v) PEG 4000, 200 mM ammonium sulfate in a 1 to 4 ratio in a total volume of 250 to 500 microlitres.

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Data collection

DiffractionMean temperature: 301 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.24 Å
DetectorType: MPCCD / Detector: CCD / Date: Oct 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.85→37.9 Å / Num. obs: 25114 / % possible obs: 100 % / Redundancy: 486 % / CC1/2: 1 / R split: 0.078 / Net I/σ(I): 10.7
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 305 % / Num. unique obs: 1226 / CC1/2: 0.67 / R split: 0.603 / % possible all: 100
Serial crystallography measurementFocal spot size: 1.675 µm2 / Pulse duration: 10 fsec. / Pulse energy: 289 µJ / XFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryDescription: Silicon fixed target / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: Oxford Chip / Sample dehydration prevention: Mylar film

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Processing

Software
NameVersionClassification
PHENIX1.15.2refinement
PDB_EXTRACT3.25data extraction
CrystFEL0.6.3data reduction
CrystFEL0.6.3data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 3ixf

3ixf


Resolution: 1.85→33.955 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2131 1221 4.87 %
Rwork0.1783 23834 -
obs0.18 25055 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.51 Å2 / Biso mean: 40.0014 Å2 / Biso min: 23.81 Å2
Refinement stepCycle: final / Resolution: 1.85→33.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2106 0 91 84 2281
Biso mean--46.62 43.34 -
Num. residues----274
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.85-1.92410.5211230.46952612
1.9241-2.01160.24811180.23652615
2.0116-2.11770.22931290.18222617
2.1177-2.25030.2381370.17672613
2.2503-2.4240.22591520.17872609
2.424-2.66790.22771180.17912655
2.6679-3.05370.22991600.18242638
3.0537-3.84650.17991170.1652699
3.8465-33.9550.19711670.16612776

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