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- PDB-5lk9: Dehaloperoxidase B from Amphitrite ornata: indazole complex -

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Basic information

Entry
Database: PDB / ID: 5lk9
TitleDehaloperoxidase B from Amphitrite ornata: indazole complex
ComponentsDehaloperoxidase B
KeywordsOXIDOREDUCTASE / indazole / dehaloperoxidase / heme
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 / 1H-indazole / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 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: indazole complex
Authors: Chicano, T.M. / Hough, M.A.
History
DepositionJul 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 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 1.2May 8, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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.pdbx_ptnr2_label_alt_id / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,86712
Polymers30,8292
Non-polymers2,03810
Water6,792377
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-68 kcal/mol
Surface area13740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.250, 68.410, 68.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(de3) / References: UniProt: Q9NAV7

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Non-polymers , 5 types, 387 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.: 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-LZ1 / 1H-indazole


Mass: 118.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.33 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 12 mg/ml protein in 20 mM cacodylate pH 6.4 Reservoir 18% PEG 4000, 200 mM ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9163 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 25, 2016
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9163 Å / Relative weight: 1
ReflectionResolution: 1.12→48.4 Å / Num. obs: 108968 / % possible obs: 98.3 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Net I/σ(I): 50.4
Reflection shellResolution: 1.12→1.15 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.926 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.576 / % possible all: 98.4

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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 / Resolution: 1.12→48.38 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.305 / SU ML: 0.025 / SU R Cruickshank DPI: 0.0311 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.031 / ESU R Free: 0.031
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1665 5388 4.9 %RANDOM
Rwork0.1429 ---
obs0.1441 103485 98.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 61.74 Å2 / Biso mean: 13.963 Å2 / Biso min: 6.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å20 Å2
2---0.21 Å20 Å2
3----0.61 Å2
Refinement stepCycle: final / Resolution: 1.12→48.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2162 0 136 380 2678
Biso mean--14.23 26.16 -
Num. residues----274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192508
X-RAY DIFFRACTIONr_bond_other_d0.0020.022301
X-RAY DIFFRACTIONr_angle_refined_deg1.7642.0193437
X-RAY DIFFRACTIONr_angle_other_deg1.52335324
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8485330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.94524.602113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7615438
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.3081513
X-RAY DIFFRACTIONr_chiral_restr0.1790.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022935
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02626
X-RAY DIFFRACTIONr_mcbond_it1.1961.1451173
X-RAY DIFFRACTIONr_mcbond_other1.1971.1461174
X-RAY DIFFRACTIONr_mcangle_it1.5971.7311479
X-RAY DIFFRACTIONr_rigid_bond_restr7.09234809
X-RAY DIFFRACTIONr_sphericity_free21.5445260
X-RAY DIFFRACTIONr_sphericity_bonded6.73554857
LS refinement shellResolution: 1.12→1.149 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 361 -
Rwork0.265 7268 -
all-7629 -
obs--94.32 %

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