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- PDB-5v5j: oxyferrous Dehaloperoxidase B -

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Basic information

Entry
Database: PDB / ID: 5v5j
Titleoxyferrous Dehaloperoxidase B
ComponentsDehaloperoxidase B
KeywordsOXYGEN TRANSPORT / peroxidase / peroxygenase / 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 / Globins / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.814 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: Biochim Biophys Acta Proteins Proteom / Year: 2018
Title: How nature tunes isoenzyme activity in the multifunctional catalytic globin dehaloperoxidase from Amphitrite ornata.
Authors: Carey, L.M. / Gavenko, R. / Svistunenko, D.A. / Ghiladi, R.A.
History
DepositionMar 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / 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 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dehaloperoxidase B
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,96315
Polymers30,8292
Non-polymers2,13413
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-56 kcal/mol
Surface area12360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.581, 67.018, 68.448
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 (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q9NAV7

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Non-polymers , 5 types, 206 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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.: 2 / Source method: obtained synthetically / Formula: O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.24 Å3/Da / Density % sol: 41.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: PEG4000, ammonium sulfate, cacodylate buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.814→50 Å / Num. obs: 24707 / % possible obs: 98.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 21.5
Reflection shellResolution: 1.814→1.859 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.623 / Num. unique obs: 1176 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IXF

3ixf


Resolution: 1.814→29.29 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.91
RfactorNum. reflection% reflectionSelection details
Rfree0.1947 2009 8.14 %random set
Rwork0.1658 ---
obs0.1683 24667 98.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.814→29.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2207 0 56 193 2456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062423
X-RAY DIFFRACTIONf_angle_d0.8663292
X-RAY DIFFRACTIONf_dihedral_angle_d15.6112099
X-RAY DIFFRACTIONf_chiral_restr0.042329
X-RAY DIFFRACTIONf_plane_restr0.004423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8138-1.85920.23631240.19671455X-RAY DIFFRACTION91
1.8592-1.90940.26151460.19671564X-RAY DIFFRACTION97
1.9094-1.96560.24311340.18261601X-RAY DIFFRACTION98
1.9656-2.0290.23571390.17641574X-RAY DIFFRACTION98
2.029-2.10150.24151410.16971602X-RAY DIFFRACTION99
2.1015-2.18560.21921470.15441595X-RAY DIFFRACTION99
2.1856-2.28510.20351430.16061621X-RAY DIFFRACTION99
2.2851-2.40550.16631380.15721626X-RAY DIFFRACTION100
2.4055-2.55610.1931480.16091632X-RAY DIFFRACTION100
2.5561-2.75340.18551440.15961631X-RAY DIFFRACTION100
2.7534-3.03020.21171500.1621647X-RAY DIFFRACTION100
3.0302-3.46810.16041450.16571667X-RAY DIFFRACTION100
3.4681-4.36710.15951500.14461683X-RAY DIFFRACTION100
4.3671-29.29430.2081600.1851760X-RAY DIFFRACTION100

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