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- PDB-6ch6: Dehaloperoxidase B in complex with substrate 2,4-dimethoxyphenol -

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Basic information

Entry
Database: PDB / ID: 6ch6
TitleDehaloperoxidase B in complex with substrate 2,4-dimethoxyphenol
ComponentsDehaloperoxidase B
KeywordsOXIDOREDUCTASE
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
2,4-dimethoxyphenol / PROTOPORPHYRIN IX CONTAINING FE / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
Authorsde Serrano, V.S. / Carey, L.M. / Ghiladi, R.A.
CitationJournal: Biochemistry / Year: 2018
Title: Peroxidase versus Peroxygenase Activity: Substrate Substituent Effects as Modulators of Enzyme Function in the Multifunctional Catalytic Globin Dehaloperoxidase.
Authors: McGuire, A.H. / Carey, L.M. / de Serrano, V. / Dali, S. / Ghiladi, R.A.
History
DepositionFeb 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 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.pdbx_ptnr1_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
Revision 1.2Dec 25, 2024Group: Derived calculations / Structure summary
Category: pdbx_entry_details / struct_conn / struct_conn_type

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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)32,68810
Polymers30,8292
Non-polymers1,8608
Water5,206289
1
A: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6578
Polymers15,4141
Non-polymers1,2437
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0312
Polymers15,4141
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.795, 66.352, 68.287
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: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9NAV7

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Non-polymers , 5 types, 297 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.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-F0J / 2,4-dimethoxyphenol


Mass: 154.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 32% PEG 3350, 0.2 M ammonium sulfate, 20 mM sodium cacodylate, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 12, 2017
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→37.23 Å / Num. obs: 29059 / % possible obs: 99.97 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 12.3 Å2 / CC1/2: 0.722 / Rpim(I) all: 0.065 / Rrim(I) all: 0.156 / Net I/σ(I): 13.81
Reflection shellResolution: 1.7→37.23 Å / Redundancy: 5 % / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 2 / Num. unique obs: 2117 / CC1/2: 0.748 / Rpim(I) all: 0.309 / Rrim(I) all: 0.719 / % possible all: 99.86

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IXF

3ixf


Resolution: 1.7→37.23 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.952 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.027 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22732 1482 4.9 %RANDOM
Rwork0.16223 ---
obs0.16539 29059 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.617 Å2
Baniso -1Baniso -2Baniso -3
1-2.48 Å20 Å20 Å2
2---15.63 Å2-0 Å2
3---13.14 Å2
Refinement stepCycle: 1 / Resolution: 1.7→37.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2154 0 124 289 2567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192916
X-RAY DIFFRACTIONr_bond_other_d0.0020.022618
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.9994016
X-RAY DIFFRACTIONr_angle_other_deg1.0862.9966152
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5135392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00924.412136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.76415541
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0821519
X-RAY DIFFRACTIONr_chiral_restr0.1250.2405
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023482
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02657
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6361.1171376
X-RAY DIFFRACTIONr_mcbond_other1.6371.1161375
X-RAY DIFFRACTIONr_mcangle_it2.21.6951787
X-RAY DIFFRACTIONr_mcangle_other2.1991.6961788
X-RAY DIFFRACTIONr_scbond_it2.5591.4731540
X-RAY DIFFRACTIONr_scbond_other2.5591.4741540
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9782.1052209
X-RAY DIFFRACTIONr_long_range_B_refined4.01115.6693774
X-RAY DIFFRACTIONr_long_range_B_other4.01115.6743775
X-RAY DIFFRACTIONr_rigid_bond_restr2.49735534
X-RAY DIFFRACTIONr_sphericity_free37.5185152
X-RAY DIFFRACTIONr_sphericity_bonded11.12255559
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 85 -
Rwork0.341 2117 -
obs--99.86 %
Refinement TLS params.

S11: 0.0049 Å ° / Method: refined / Origin x: 0 Å / Origin y: 0 Å / Origin z: 0 Å / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)
10.05010.02550.00660.0310.00730.0378-0.0112-0.0060.012-0.0056-0.00540.0090.00650.00070.03690.0007-0.00160.03470.00120.0011
20.0208-0.00170.00730.07330.01880.01070.002-0.0107-0.00070.0006-0.005-0.00640.001-0.00560.0232-0.0002-0.00310.0322-0.00020.0061
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 38
2X-RAY DIFFRACTION1A39 - 90
3X-RAY DIFFRACTION1A91 - 137
4X-RAY DIFFRACTION2B1 - 31
5X-RAY DIFFRACTION2B32 - 87
6X-RAY DIFFRACTION2B88 - 137

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