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- PDB-6ch5: Dehaloperoxidase B in complex with substrate 4-Nitroguaiacol -

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Basic information

Entry
Database: PDB / ID: 6ch5
TitleDehaloperoxidase B in complex with substrate 4-Nitroguaiacol
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 domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2-methoxy-4-nitrophenol / PROTOPORPHYRIN IX CONTAINING FE / DI(HYDROXYETHYL)ETHER / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 21, 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.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)33,09414
Polymers30,8292
Non-polymers2,26512
Water4,684260
1
A: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,87510
Polymers15,4141
Non-polymers1,4609
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2194
Polymers15,4141
Non-polymers8053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.649, 66.367, 68.218
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 , 6 types, 272 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.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-F0M / 2-methoxy-4-nitrophenol / 4-Nitroguaiacol


Mass: 169.135 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7NO4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.19 Å3/Da / Density % sol: 43.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 3350, ammonium sulfate,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 / Details: double-crystal monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→44.36 Å / Num. obs: 31440 / % possible obs: 99.3 % / Observed criterion σ(I): 3 / Redundancy: 4.3 % / Biso Wilson estimate: 12.5 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 19.776
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.326 / % possible all: 96.8

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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: 1.65→44.36 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.318 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.023 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1582 4.8 %RANDOM
Rwork0.153 ---
obs0.155 31440 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2--1.65 Å20 Å2
3----2.04 Å2
Refinement stepCycle: LAST / Resolution: 1.65→44.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2139 0 148 260 2547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193018
X-RAY DIFFRACTIONr_bond_other_d0.0020.022662
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.9994166
X-RAY DIFFRACTIONr_angle_other_deg1.0532.9916264
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7185404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64724.752141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.40615543
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4261518
X-RAY DIFFRACTIONr_chiral_restr0.1260.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023653
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02676
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_it1.5571.161414
X-RAY DIFFRACTIONr_mcbond_other1.5581.161413
X-RAY DIFFRACTIONr_mcangle_it1.961.7511848
X-RAY DIFFRACTIONr_mcangle_other1.961.7521849
X-RAY DIFFRACTIONr_scbond_it2.0911.4771604
X-RAY DIFFRACTIONr_scbond_other2.0911.4771604
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7092.1372297
X-RAY DIFFRACTIONr_long_range_B_refined3.46615.6813877
X-RAY DIFFRACTIONr_long_range_B_other3.46515.6843878
X-RAY DIFFRACTIONr_rigid_bond_restr2.0435680
X-RAY DIFFRACTIONr_sphericity_free22.985138
X-RAY DIFFRACTIONr_sphericity_bonded8.08355683
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 124 -
Rwork0.287 2214 -
obs--96.81 %

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