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- PDB-7acp: Serial synchrotron structure of dehaloperoxidase B -

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Basic information

Entry
Database: PDB / ID: 7acp
TitleSerial synchrotron structure of dehaloperoxidase B
ComponentsDehaloperoxidase B
KeywordsOXIDOREDUCTASE / SSX / serial crystallography / dehaloperoxidase / peroxidase / fixed-target
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 / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMoreno Chicano, T. / Ebrahim, A. / Axford, D.A. / Sherrell, D.A. / 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. / 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 11, 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 ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 15, 2025Group: Database references / Structure summary
Category: audit_author / citation_author / pdbx_entry_details
Item: _audit_author.name / _citation_author.name / _pdbx_entry_details.has_protein_modification

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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
Water3,117173
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)16,1622
Polymers15,5461
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.180, 66.995, 68.932
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.: 173 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.27 Å3/Da / Density % sol: 45.86 % / Description: Microcrystals
Crystal growTemperature: 277 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 ml.

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.45→68.9 Å / Num. obs: 52472 / % possible obs: 100 % / Redundancy: 104 % / Biso Wilson estimate: 14.2 Å2 / CC1/2: 0.98 / R split: 0.121 / Net I/σ(I): 3.8
Reflection shellResolution: 1.45→1.48 Å / Num. unique obs: 2504 / CC1/2: 0.977
Serial crystallography sample deliveryDescription: silicon 'Oxford' chip / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: silicon 'oxford' chip / Sample dehydration prevention: mylar film / Sample solvent: mother liquor

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Processing

Software
NameVersionClassification
PHENIX1.1.15refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
DIALSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ixf

3ixf


Resolution: 1.45→34.466 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2089 2622 5.16 %
Rwork0.1671 48226 -
obs0.1693 50848 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.84 Å2 / Biso mean: 26.2887 Å2 / Biso min: 9.79 Å2
Refinement stepCycle: final / Resolution: 1.45→34.466 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2127 0 96 173 2396
Biso mean--38.79 36.76 -
Num. residues----274
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.45-1.47640.33761310.27432499100
1.4764-1.50480.32881540.25792496100
1.5048-1.53550.31261250.24252527100
1.5355-1.56890.33391490.2512511100
1.5689-1.60540.28291120.24532515100
1.6054-1.64550.36381260.2809246498
1.6455-1.690.32051540.24482484100
1.69-1.73970.2891450.22452517100
1.7397-1.79590.31661160.20992536100
1.7959-1.86010.2292930.19832583100
1.8601-1.93450.26361240.18212524100
1.9345-2.02260.23651510.16762515100
2.0226-2.12920.21471340.15682539100
2.1292-2.26260.22251610.14642521100
2.2626-2.43720.16881470.14472551100
2.4372-2.68240.19241280.14312573100
2.6824-3.07030.19961870.15192538100
3.0703-3.86750.16621470.13942596100
3.8675-34.4660.15111380.14512737100

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