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- PDB-6i6g: Dehaloperoxidase B from Amphitrite ornata - complex with 5-bromoindole -

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Basic information

Entry
Database: PDB / ID: 6i6g
TitleDehaloperoxidase B from Amphitrite ornata - complex with 5-bromoindole
ComponentsDehaloperoxidase B
KeywordsOXIDOREDUCTASE / 5-bromoindole / Peroxidase / Globin
Function / homology
Function and homology information


oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin-like, M family globin domain / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
5-bromanyl-1~{H}-indole / 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. / Worrall, J.A.R. / Strange, R.W. / Axford, D. / Sherrell, D.A. / Sugimoto, H. / Tono, K. / Owada, S. / Duyvesteyn, H.
CitationJournal: Iucrj / Year: 2019
Title: High-throughput structures of protein-ligand complexes at room temperature using serial femtosecond crystallography.
Authors: Moreno-Chicano, T. / Ebrahim, A. / Axford, D. / Appleby, M.V. / Beale, J.H. / Chaplin, A.K. / Duyvesteyn, H.M.E. / Ghiladi, R.A. / Owada, S. / Sherrell, D.A. / Strange, R.W. / Sugimoto, H. / ...Authors: Moreno-Chicano, T. / Ebrahim, A. / Axford, D. / Appleby, M.V. / Beale, J.H. / Chaplin, A.K. / Duyvesteyn, H.M.E. / Ghiladi, R.A. / Owada, S. / Sherrell, D.A. / Strange, R.W. / Sugimoto, H. / Tono, K. / Worrall, J.A.R. / Owen, R.L. / Hough, M.A.
History
DepositionNov 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)32,6468
Polymers30,8292
Non-polymers1,8176
Water2,000111
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-57 kcal/mol
Surface area12680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.000, 67.330, 68.760
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: 15414.462 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-H4N / 5-bromanyl-1~{H}-indole


Mass: 196.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H6BrN
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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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: 46.29 % / Description: Microcrystals
Crystal growTemperature: 277 K / Method: batch mode / pH: 6
Details: 5.5 mg/ml DHP-B in 20 mM MES pH 6.0 mixed with 35% PEG 4000, 200mM AmSO4 at a ratio of 1:4 in a total volume of 250 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 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.85→45.631 Å / Num. obs: 24840 / % possible obs: 100 % / Redundancy: 908 % / CC1/2: 1 / R split: 0.055 / Net I/σ(I): 12
Reflection shellResolution: 1.85→1.9 Å / Mean I/σ(I) obs: 1.56 / CC1/2: 0.65 / R split: 0.66 / % possible all: 100
Serial crystallography measurementCollection time total: 80 hours / Focal spot size: 1.66 µm2 / Pulse duration: 10 fsec. / Pulse energy: 289 µJ / Pulse photon energy: 10.01 keV / XFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryDescription: Silicon nitride fixed target / Method: fixed target
Serial crystallography sample delivery fixed targetSample dehydration prevention: Mylar film / Sample solvent: Mother liquor

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.24data extraction
CrystFELdata reduction
CrystFELdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ixf

3ixf


Resolution: 1.85→45.631 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.38
RfactorNum. reflection% reflection
Rfree0.1891 1260 5.08 %
Rwork0.1668 --
obs0.1679 24781 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.09 Å2 / Biso mean: 44.1014 Å2 / Biso min: 27.29 Å2
Refinement stepCycle: final / Resolution: 1.85→45.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2105 0 176 111 2392
Biso mean--48.21 45.51 -
Num. residues----274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052323
X-RAY DIFFRACTIONf_angle_d0.9643165
X-RAY DIFFRACTIONf_chiral_restr0.035320
X-RAY DIFFRACTIONf_plane_restr0.003406
X-RAY DIFFRACTIONf_dihedral_angle_d10.9721350
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.85-1.92410.42751340.399625542688
1.9241-2.01170.23811470.224125572704
2.0117-2.11770.20391240.174125972721
2.1177-2.25040.18981540.176425812735
2.2504-2.42420.19321450.169125822727
2.4242-2.66810.20371570.166925802737
2.6681-3.05410.21440.171526222766
3.0541-3.84750.16861230.153926642787
3.8475-45.64540.17151320.154827842916

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