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- PDB-7kfm: Room temperature oxyferrous Dehaloperoxidase B -

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Basic information

Entry
Database: PDB / ID: 7kfm
TitleRoom temperature oxyferrous Dehaloperoxidase B
ComponentsDehaloperoxidase B
KeywordsMETAL BINDING PROTEIN
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 / OXYGEN MOLECULE / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsCarey, L.M. / Ghiladi, R.A.
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 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 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 18, 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)32,4068
Polymers30,8292
Non-polymers1,5776
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.976, 66.883, 69.156
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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) / Plasmid: pET28a
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9NAV7

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Non-polymers , 5 types, 128 molecules

#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: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 46.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: MPEG 2000, 200 mM ammonium sulfate, cacodylate buffer

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 28964 / % possible obs: 99.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 34.9
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1451 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IXF

3ixf


Resolution: 1.75→37.753 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.24
RfactorNum. reflection% reflection
Rfree0.1939 1997 6.91 %
Rwork0.1648 --
obs0.1668 28918 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→37.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2108 0 106 122 2336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072421
X-RAY DIFFRACTIONf_angle_d0.8823311
X-RAY DIFFRACTIONf_dihedral_angle_d26.817863
X-RAY DIFFRACTIONf_chiral_restr0.043337
X-RAY DIFFRACTIONf_plane_restr0.004432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.79350.3091390.26891857X-RAY DIFFRACTION98
1.7935-1.8420.26591400.22551918X-RAY DIFFRACTION100
1.842-1.89620.23511460.19911915X-RAY DIFFRACTION100
1.8962-1.95740.2521390.19041907X-RAY DIFFRACTION100
1.9574-2.02730.25641410.18341917X-RAY DIFFRACTION100
2.0273-2.10850.22441450.18591925X-RAY DIFFRACTION100
2.1085-2.20450.21031410.17681912X-RAY DIFFRACTION100
2.2045-2.32070.20751420.17481934X-RAY DIFFRACTION100
2.3207-2.4660.19471440.17341935X-RAY DIFFRACTION100
2.466-2.65640.24071450.17891922X-RAY DIFFRACTION100
2.6564-2.92360.19021460.1811929X-RAY DIFFRACTION99
2.9236-3.34650.21481380.17361939X-RAY DIFFRACTION99
3.3465-4.21530.14871470.13881934X-RAY DIFFRACTION98
4.2153-37.7530.15211440.13141977X-RAY DIFFRACTION95

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