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- PDB-5llz: Dehaloperoxidase B from Amphitrite ornata: benzotriazole complex -

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Basic information

Entry
Database: PDB / ID: 5llz
TitleDehaloperoxidase B from Amphitrite ornata: benzotriazole complex
ComponentsDehaloperoxidase B
KeywordsOXIDOREDUCTASE / benzotriazole / dehaloperoxidase / heme
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 domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1H-benzotriazole / PROTOPORPHYRIN IX CONTAINING FE / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsChicano, T.M. / Dworkowski, F.S.N. / Hough, M.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Leverhulme TrustRPG-2014-355 United Kingdom
CitationJournal: to be published
Title: Dehaloperoxidase B from Amphitrite ornata: benzotriazole complex
Authors: Chicano, T.M. / Hough, M.A.
History
DepositionJul 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Author supporting evidence / Data collection / Derived calculations
Category: pdbx_audit_support / struct_conn / struct_conn_type
Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)32,66110
Polymers30,8292
Non-polymers1,8328
Water7,188399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-70 kcal/mol
Surface area13930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.680, 67.070, 69.010
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 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.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-0CT / 1H-benzotriazole


Mass: 119.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5N3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / 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: 2.28 Å3/Da / Density % sol: 45.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.4
Details: 12 mg/ml DHP B in 20 mM Na cacodylate (pH 6.4) was mixed with a reservoir solution comprising 14-20% (w/v) PEG 4000 and 150-250 mM ammonium sulfate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 20, 2015
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.14→45.6 Å / Num. obs: 100913 / % possible obs: 98 % / Redundancy: 4 % / CC1/2: 1 / Rmerge(I) obs: 0.037 / Net I/σ(I): 17.6
Reflection shellResolution: 1.14→1.17 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.801 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.571 / % possible all: 95.3

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ixf

3ixf


Resolution: 1.14→45.57 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.475 / SU ML: 0.029 / SU R Cruickshank DPI: 0.0337 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.036
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1794 4962 4.9 %RANDOM
Rwork0.1436 ---
obs0.1453 95874 97.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 99.84 Å2 / Biso mean: 18.354 Å2 / Biso min: 9.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2---0.12 Å20 Å2
3---0.36 Å2
Refinement stepCycle: final / Resolution: 1.14→45.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2162 0 120 402 2684
Biso mean--25.95 30.99 -
Num. residues----274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192508
X-RAY DIFFRACTIONr_bond_other_d0.0020.022266
X-RAY DIFFRACTIONr_angle_refined_deg1.9672.013431
X-RAY DIFFRACTIONr_angle_other_deg1.68535229
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0625316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.66724.561114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.39215432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1081514
X-RAY DIFFRACTIONr_chiral_restr0.1430.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022977
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02623
X-RAY DIFFRACTIONr_mcbond_it1.7831.5011199
X-RAY DIFFRACTIONr_mcbond_other1.7771.51198
X-RAY DIFFRACTIONr_mcangle_it2.2642.2641526
X-RAY DIFFRACTIONr_rigid_bond_restr3.46634774
X-RAY DIFFRACTIONr_sphericity_free25.7245291
X-RAY DIFFRACTIONr_sphericity_bonded11.03654816
LS refinement shellResolution: 1.14→1.17 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 388 -
Rwork0.282 6786 -
all-7174 -
obs--94.91 %

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