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- PDB-5vlx: Dehaloperoxidase B mutant F21W -

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Basic information

Entry
Database: PDB / ID: 5vlx
TitleDehaloperoxidase B mutant F21W
ComponentsDehaloperoxidase B
Keywordsheme binding protein / mutant / peroxidase / peroxygenase / globin
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 / Globins / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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: J. Biol. Inorg. Chem. / Year: 2018
Title: Selective tuning of activity in a multifunctional enzyme as revealed in the F21W mutant of dehaloperoxidase B from Amphitrite ornata.
Authors: Carey, L.M. / Kim, K.B. / McCombs, N.L. / Swartz, P. / Kim, C. / Ghiladi, R.A.
History
DepositionApr 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Jul 21, 2021Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)32,89312
Polymers30,9072
Non-polymers1,98610
Water3,873215
1
A: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4466
Polymers15,4531
Non-polymers9935
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4466
Polymers15,4531
Non-polymers9935
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.479, 67.130, 67.368
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dehaloperoxidase B


Mass: 15453.497 Da / Num. of mol.: 2 / Mutation: F21W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amphitrite ornata (invertebrata) / Plasmid: pET16b / Production host: Escherichia coli BL21(DE3) (bacteria) / 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.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.21 Å3/Da / Density % sol: 42.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: PEG 4000, ammonium phosphate, sodium cacodylate buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 25631 / % possible obs: 97.8 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 25
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.395 / Num. unique obs: 1032 / % possible all: 80.2

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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: 1.8→18.691 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2044 2002 7.83 %
Rwork0.1662 --
obs0.1692 25584 97.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→18.691 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2213 0 44 215 2472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072421
X-RAY DIFFRACTIONf_angle_d0.9263299
X-RAY DIFFRACTIONf_dihedral_angle_d28.757863
X-RAY DIFFRACTIONf_chiral_restr0.043327
X-RAY DIFFRACTIONf_plane_restr0.004422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.84120.29751190.21591338X-RAY DIFFRACTION79
1.8412-1.89090.28361310.20741556X-RAY DIFFRACTION92
1.8909-1.94650.24941390.20251645X-RAY DIFFRACTION97
1.9465-2.00930.24071430.18521706X-RAY DIFFRACTION100
2.0093-2.0810.23081430.16451674X-RAY DIFFRACTION100
2.081-2.16420.21591500.16351742X-RAY DIFFRACTION100
2.1642-2.26260.20841400.15991685X-RAY DIFFRACTION100
2.2626-2.38160.24991450.15751726X-RAY DIFFRACTION100
2.3816-2.53050.19371430.161693X-RAY DIFFRACTION100
2.5305-2.72530.23511480.17461723X-RAY DIFFRACTION100
2.7253-2.99860.20131460.16821728X-RAY DIFFRACTION100
2.9986-3.43020.20431450.17471749X-RAY DIFFRACTION100
3.4302-4.31290.16681500.14231780X-RAY DIFFRACTION100
4.3129-18.69160.17541600.16821837X-RAY DIFFRACTION100

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