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- PDB-6cke: Dehaloperoxidase B in complex with 4-Br-guaiacol -

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Basic information

Entry
Database: PDB / ID: 6cke
TitleDehaloperoxidase B in complex with 4-Br-guaiacol
ComponentsDehaloperoxidase B
KeywordsMETAL BINDING PROTEIN / peroxidase / peroxygenase / substrate
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
4-bromo-2-methoxyphenol / PROTOPORPHYRIN IX CONTAINING FE / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsCarey, L.M. / Ghiladi, R.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1150709 United States
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 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,4577
Polymers30,8292
Non-polymers1,6285
Water7,440413
1
A: Dehaloperoxidase B
hetero molecules

B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4577
Polymers30,8292
Non-polymers1,6285
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y+1/2,-z-1/21
Buried area3220 Å2
ΔGint-75 kcal/mol
Surface area13200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.399, 66.454, 68.207
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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-Gold(DE3)pLysS AG' (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-3Z7 / 4-bromo-2-methoxyphenol


Mass: 203.033 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7BrO2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 2.1 Å3/Da / Density % sol: 41.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: PEG 3350, ammonium sulfate, sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.37→29 Å / Num. obs: 57274 / % possible obs: 99.9 % / Redundancy: 4.8 % / CC1/2: 0.746 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.037 / Net I/σ(I): 22.4
Reflection shellResolution: 1.37→1.41 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.662 / Num. unique obs: 2821 / Rpim(I) all: 0.339 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IXF

3ixf


Resolution: 1.37→29 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.08
RfactorNum. reflection% reflection
Rfree0.1927 1998 3.49 %
Rwork0.1742 --
obs0.1749 57212 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.37→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2206 0 20 413 2639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062570
X-RAY DIFFRACTIONf_angle_d0.8983528
X-RAY DIFFRACTIONf_dihedral_angle_d10.2871966
X-RAY DIFFRACTIONf_chiral_restr0.07351
X-RAY DIFFRACTIONf_plane_restr0.004469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.4050.27841400.25193837X-RAY DIFFRACTION99
1.405-1.4430.26911400.23743909X-RAY DIFFRACTION100
1.443-1.48550.23911410.21553909X-RAY DIFFRACTION100
1.4855-1.53340.21731480.1993889X-RAY DIFFRACTION100
1.5334-1.58820.21121330.18573908X-RAY DIFFRACTION100
1.5882-1.65180.22751470.18413917X-RAY DIFFRACTION100
1.6518-1.7270.19121380.18423899X-RAY DIFFRACTION100
1.727-1.8180.21761440.17723927X-RAY DIFFRACTION100
1.818-1.93190.18821430.17293941X-RAY DIFFRACTION100
1.9319-2.0810.22561380.17033949X-RAY DIFFRACTION100
2.081-2.29040.18461450.16623975X-RAY DIFFRACTION100
2.2904-2.62160.16311430.16713974X-RAY DIFFRACTION100
2.6216-3.30220.2111450.17164028X-RAY DIFFRACTION100
3.3022-290.15541530.15534152X-RAY DIFFRACTION99

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