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- PDB-7kcu: Joint neutron/X-ray structure of Oxyferrous Dehaloperoxidase B -

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Basic information

Entry
Database: PDB / ID: 7kcu
TitleJoint neutron/X-ray structure of Oxyferrous Dehaloperoxidase B
ComponentsDehaloperoxidase B
KeywordsOXIDOREDUCTASE / peroxidase / oxyferrous
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 / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCarey, L.M. / Ghiladi, R.A. / Meilleur, F. / Myles, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1150709 United States
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
DepositionOct 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 9, 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 1.2Oct 25, 2023Group: 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)32,2867
Polymers30,8292
Non-polymers1,4575
Water1,67593
1
A: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1594
Polymers15,4141
Non-polymers7453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1273
Polymers15,4141
Non-polymers7132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.830, 67.100, 69.040
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-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.4 / Details: 2000 MPEG, ammonium sulfate, cacodylate

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12981N
22981N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
NUCLEAR REACTORORNL High Flux Isotope Reactor CG4D12.8-4.6
SEALED TUBERIGAKU MICROMAX-00721.54
Detector
TypeIDDetectorDate
MAATEL IMAGINE1IMAGE PLATEFeb 24, 2017
RIGAKU RAXIS IV++2IMAGE PLATEFeb 24, 2017
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LAUELneutron1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
12.81
24.61
31.541
Reflection

Entry-ID: 7KCU

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rpim(I) allDiffraction-IDNet I/σ(I)CC1/2Rmerge(I) obs
2.2-17.481126779.35.50.10614.7
1.95-48.132111799.520.022226.80.9990.022
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsRpim(I) allDiffraction-ID% possible allRmerge(I) obsCC1/2Rrim(I) all
2.2-2.322.213270.201165.6
1.95-2.021.920770.135298.40.1350.9380.191

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
SCALAdata scaling
LAUEGENdata reduction
Refinement

Cross valid method: THROUGHOUT / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Method to determine structureStarting modelResolution (Å)Refine-IDBiso max (Å2)Biso mean (Å2)Biso min (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection Rfree (%)% reflection obs (%)SU MLσ(F)Phase error
MOLECULAR REPLACEMENT5V5J

5v5j

2.2-17.435X-RAY DIFFRACTION104.9735.34258.60.21230.15460.1604148013323148031099.720.231.3820.58
2.215-17.484NEUTRON DIFFRACTION0.30490.24910.254811271126310.0177.440
Refinement stepCycle: final / Resolution: 2.2→17.435 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2112 0 158 142 2412
Biso mean--46.39 40.72 -
Num. residues----274
LS refinement shell

Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2154-2.3160.37641080.3206972NEUTRON DIFFRACTION60
2.316-2.43780.38581230.32471114NEUTRON DIFFRACTION70
2.4378-2.590.32221270.27351141NEUTRON DIFFRACTION71
2.59-2.78930.29621330.27491184NEUTRON DIFFRACTION73
2.7893-3.06860.31121400.25031265NEUTRON DIFFRACTION78
3.0686-3.50950.31021540.24671378NEUTRON DIFFRACTION84
3.5095-4.40990.25641660.21731499NEUTRON DIFFRACTION90
4.4099-17.4840.28091760.20391583NEUTRON DIFFRACTION91
2.2-2.27090.26751300.18441172X-RAY DIFFRACTION99
2.2709-2.35190.27381330.18211193X-RAY DIFFRACTION100
2.3519-2.44580.2671300.17841173X-RAY DIFFRACTION99
2.4458-2.55680.23981350.15951205X-RAY DIFFRACTION100
2.5568-2.69110.23961320.16721204X-RAY DIFFRACTION100
2.6911-2.8590.21061340.17141197X-RAY DIFFRACTION100
2.859-3.07870.21391350.17621213X-RAY DIFFRACTION100
3.0787-3.38640.22121330.17171204X-RAY DIFFRACTION100
3.3864-3.87180.20311370.14331224X-RAY DIFFRACTION100
3.8718-4.86040.1771380.1211238X-RAY DIFFRACTION100
4.8604-17.4350.181430.14171300X-RAY DIFFRACTION99

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