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- PDB-7adx: SFX structure of dehaloperoxidase B in the oxyferrous form -

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Basic information

Entry
Database: PDB / ID: 7adx
TitleSFX structure of dehaloperoxidase B in the oxyferrous form
ComponentsDehaloperoxidase B
KeywordsOXIDOREDUCTASE / oxyferrous / ferrous / serial crystallography / oxygen
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 / OXYGEN MOLECULE / 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. / Worrall, J.W. / Axford, D.A. / Owada, S. / Tosha, T. / Sugimoto, H. / 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 from Amphitrite ornata in the oxyferrous form
Authors: Moreno Chicano, T. / Ebrahim, A. / Worrall, J.W. / Axford, D.A. / Owada, S. / Tosha, T. / Sugimoto, H. / Strange, R.W. / Owen, R.L. / Hough, M.A.
History
DepositionSep 16, 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)32,5487
Polymers31,0912
Non-polymers1,4575
Water1,53185
1
A: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3544
Polymers15,5461
Non-polymers8093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1943
Polymers15,5461
Non-polymers6482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.310, 68.100, 68.330
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: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 277 K / Method: batch mode / pH: 6
Details: DHP in 20 mM MES pH 6 mixed with 40% PEG 4000, 200 mM ammonium sulfate in 1 to 4 ratio with 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: 1.13 Å
DetectorType: MPCCD / Detector: CCD / Date: Jun 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.13 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.596
11-H, -L, -K20.404
ReflectionResolution: 1.85→48.24 Å / Num. obs: 25099 / % possible obs: 100 % / Redundancy: 322 % / Biso Wilson estimate: 28.1 Å2 / CC1/2: 0.98 / R split: 0.12 / Net I/σ(I): 6.8
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 224 % / Num. unique obs: 1213 / CC1/2: 0.5 / R split: 0.6 / % possible all: 100
Serial crystallography measurementPulse duration: 10 fsec. / XFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryDescription: fixed target / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: Oxford Chip / Sample dehydration prevention: mylar film / Sample holding: Silicon chip / Sample solvent: mother liquor / Support base: xy stage

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
PDB_EXTRACT3.25data extraction
CrystFEL0.6.3data reduction
CrystFEL0.6.3data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ixf

3ixf


Resolution: 1.85→45.63 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.761 / SU ML: 0.056 / SU R Cruickshank DPI: 0.0262 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1912 1236 4.9 %RANDOM
Rwork0.1653 ---
obs0.1665 23811 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.61 Å2 / Biso mean: 29.76 Å2 / Biso min: 17.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å2-0 Å2-0 Å2
2--6.37 Å20 Å2
3----7.13 Å2
Refinement stepCycle: final / Resolution: 1.85→45.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2106 0 93 85 2284
Biso mean--36.21 36.26 -
Num. residues----274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132277
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182042
X-RAY DIFFRACTIONr_angle_refined_deg1.6251.7053093
X-RAY DIFFRACTIONr_angle_other_deg1.2951.6224677
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8915278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.70523.091110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.78115368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8371511
X-RAY DIFFRACTIONr_chiral_restr0.0770.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022657
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02563
LS refinement shellResolution: 1.845→1.893 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 89 -
Rwork0.391 1555 -
all-1644 -
obs--89.93 %

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