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- PDB-7adq: Serial Laue crystallography structure of dehaloperoxidase B from ... -

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Basic information

Entry
Database: PDB / ID: 7adq
TitleSerial Laue crystallography structure of dehaloperoxidase B from Amphitrite ornata
ComponentsDehaloperoxidase B
KeywordsOXIDOREDUCTASE / serial Laue / microcrystal / multifunctional globin
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsMoreno-Chicano, T.M. / Ebrahim, A.E. / Srajer, V. / Henning, R.W. / Doak, B.C. / Trebbin, M. / Monteiro, D.C.F. / Hough, M.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R006008/1 United Kingdom
CitationJournal: Iucrj / Year: 2022
Title: Complementarity of neutron, XFEL and synchrotron crystallography for defining the structures of metalloenzymes at room temperature.
Authors: Moreno-Chicano, T. / Carey, L.M. / Axford, D. / Beale, J.H. / Doak, R.B. / Duyvesteyn, H.M.E. / Ebrahim, A. / Henning, R.W. / Monteiro, D.C.F. / Myles, D.A. / Owada, S. / Sherrell, D.A. / ...Authors: Moreno-Chicano, T. / Carey, L.M. / Axford, D. / Beale, J.H. / Doak, R.B. / Duyvesteyn, H.M.E. / Ebrahim, A. / Henning, R.W. / Monteiro, D.C.F. / Myles, D.A. / Owada, S. / Sherrell, D.A. / Straw, M.L. / Srajer, V. / Sugimoto, H. / Tono, K. / Tosha, T. / Tews, I. / Trebbin, M. / Strange, R.W. / Weiss, K.L. / Worrall, J.A.R. / Meilleur, F. / Owen, R.L. / Ghiladi, R.A. / Hough, M.A.
History
DepositionSep 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 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
Water2,522140
1
A: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2583
Polymers15,5461
Non-polymers7132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2583
Polymers15,5461
Non-polymers7132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.800, 67.300, 67.500
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.22 Å3/Da / Density % sol: 44.62 %
Crystal growTemperature: 277 K / Method: batch mode / pH: 6
Details: 30 mg per ml DHP mixed with 200 mM ammonium sulfate 40 percent PEG 4000, in a 1 to 4 ratio in a total volume of 250 to 500 microlitres

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.815-0.863
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Apr 19, 2017
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray / Wavelength: 0.815-0.863
Radiation wavelength
IDWavelength (Å)Relative weight
10.8151
20.8631
ReflectionResolution: 2→47.7 Å / Num. obs: 12928 / % possible obs: 67.8 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 34.1
Reflection shellResolution: 2→2.09 Å / Redundancy: 7.8 % / Num. unique obs: 513 / % possible all: 22
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetDescription: Heidelberg chip

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Processing

Software
NameVersionClassification
PHENIXv1.1.18refinement
PDB_EXTRACT3.25data extraction
Precognitiondata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ixf

3ixf


Resolution: 2.01→47.66 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0.23 / Phase error: 16.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2152 651 5.05 %
Rwork0.1623 12251 -
obs0.165 12902 67.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 49.38 Å2 / Biso mean: 15.1775 Å2 / Biso min: 1.89 Å2
Refinement stepCycle: final / Resolution: 2.01→47.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2083 0 91 140 2314
Biso mean--17.76 18.39 -
Num. residues----274
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.01-2.160.2513580.17641130118832
2.16-2.380.2511110.17851979209056
2.38-2.720.22471350.17322613274872
2.72-3.430.22061640.16573100326485
3.43-47.660.18971830.14763429361290

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