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- PDB-5k1l: Dehaloperoxidase B from Amphitrite ornata: benzimidazole complex -

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Basic information

Entry
Database: PDB / ID: 5k1l
TitleDehaloperoxidase B from Amphitrite ornata: benzimidazole complex
ComponentsDehaloperoxidase B
KeywordsOXIDOREDUCTASE / globin / peroxidase / benzimidazole / azole
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
BENZIMIDAZOLE / PROTOPORPHYRIN IX CONTAINING FE / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsMoreno Chicano, T. / Hough, M.A.
Funding support United Kingdom, United States, 2items
OrganizationGrant numberCountry
Leverhulme TrustRPG-2014-355 United Kingdom
National Science FoundationCHE-1150709 United States
CitationJournal: to be published
Title: Dehaloperoxidase B from Amphitrite ornata: benzimidazole complex
Authors: Moreno Chicano, T. / Hough, M.A.
History
DepositionMay 18, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / struct_conn / struct_conn_type
Item: _citation.title / _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 2024Group: Advisory / Data collection ...Advisory / 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 / 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.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)32,5869
Polymers30,8292
Non-polymers1,7577
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-57 kcal/mol
Surface area13720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.790, 68.300, 68.530
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-BZI / BENZIMIDAZOLE


Mass: 118.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6N2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.31 Å3/Da / Density % sol: 46.69 % / Description: Prism
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 15 % PEG 4000 150 mM Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 24, 2016
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.08→45.41 Å / Num. obs: 122447 / % possible obs: 99.8 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Net I/σ(I): 16.7
Reflection shellResolution: 1.08→1.11 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.44 / Mean I/σ(I) obs: 1.2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IXF

3ixf


Resolution: 1.08→45.41 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.144 / SU ML: 0.024 / SU R Cruickshank DPI: 0.0285 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.028 / ESU R Free: 0.03
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1772 6171 5 %RANDOM
Rwork0.1507 ---
obs0.1521 116192 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 92.74 Å2 / Biso mean: 17.915 Å2 / Biso min: 8.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2---0.88 Å20 Å2
3---0.36 Å2
Refinement stepCycle: final / Resolution: 1.08→45.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2162 0 119 308 2589
Biso mean--20.73 27.95 -
Num. residues----274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192477
X-RAY DIFFRACTIONr_bond_other_d0.0020.022248
X-RAY DIFFRACTIONr_angle_refined_deg1.7512.0153398
X-RAY DIFFRACTIONr_angle_other_deg2.06435191
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4455323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.6124.609115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6415425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.3071514
X-RAY DIFFRACTIONr_chiral_restr0.1450.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022935
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02621
X-RAY DIFFRACTIONr_mcbond_it2.4591.6121171
X-RAY DIFFRACTIONr_mcbond_other2.4591.6121170
X-RAY DIFFRACTIONr_mcangle_it2.8682.4291481
X-RAY DIFFRACTIONr_rigid_bond_restr6.30534725
X-RAY DIFFRACTIONr_sphericity_free28.612564
X-RAY DIFFRACTIONr_sphericity_bonded11.42554892
LS refinement shellResolution: 1.08→1.108 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 483 -
Rwork0.286 8500 -
all-8983 -
obs--99.77 %

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