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- PDB-7lzk: DHP B in complex with 2,4-Dichlorophenol substrate -

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Basic information

Entry
Database: PDB / ID: 7lzk
TitleDHP B in complex with 2,4-Dichlorophenol substrate
ComponentsDehaloperoxidase B
KeywordsOXIDOREDUCTASE / peroxidase / peroxygenase / complex
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 / Globin / Globin / Globin-like superfamily
Similarity search - Domain/homology
2,4-dichlorophenol / PROTOPORPHYRIN IX CONTAINING FE / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 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: To Be Published
Title: Mechanistic and Structural Studies of 2,4-dihalophenol: Bridging the Functional Gap between Reactivity and Inhibition in Dehaloperoxidase
Authors: Carey, L.M. / Ghiladi, R.A.
History
DepositionMar 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)32,6729
Polymers30,8292
Non-polymers1,8437
Water5,350297
1
A: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1943
Polymers15,4141
Non-polymers7792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4786
Polymers15,4141
Non-polymers1,0645
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.015, 66.211, 69.969
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 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9NAV7

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Non-polymers , 5 types, 304 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C34H32FeN4O4
#3: Chemical ChemComp-5JC / 2,4-dichlorophenol / 2,4-Dichlorophenol


Mass: 163.001 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H4Cl2O
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.06 Å3/Da / Density % sol: 40.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: PEG 4000, ammonium sulfate, sodium cacodylate pH 6.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. obs: 42731 / % possible obs: 96.1 % / Redundancy: 5 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 19.94
Reflection shellResolution: 1.49→1.52 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2116 / % possible all: 96.7

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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: 1.49→29.925 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 16.63
RfactorNum. reflection% reflection
Rfree0.1873 1990 4.66 %
Rwork0.143 --
obs0.145 42698 95.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.49→29.925 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2215 0 34 297 2546
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052492
X-RAY DIFFRACTIONf_angle_d0.9273406
X-RAY DIFFRACTIONf_dihedral_angle_d12.9831565
X-RAY DIFFRACTIONf_chiral_restr0.067341
X-RAY DIFFRACTIONf_plane_restr0.004444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.51930.20781360.15542653X-RAY DIFFRACTION90
1.5193-1.56030.22711390.1442919X-RAY DIFFRACTION96
1.5603-1.60620.20221410.14072889X-RAY DIFFRACTION97
1.6062-1.65810.19591400.13082894X-RAY DIFFRACTION96
1.6581-1.71730.19491450.13382908X-RAY DIFFRACTION96
1.7173-1.78610.18251350.12862892X-RAY DIFFRACTION96
1.7861-1.86740.21390.13122896X-RAY DIFFRACTION96
1.8674-1.96580.19141460.13272921X-RAY DIFFRACTION96
1.9658-2.08890.15691410.13432903X-RAY DIFFRACTION97
2.0889-2.25020.1811460.1372931X-RAY DIFFRACTION97
2.2502-2.47650.1991450.13992963X-RAY DIFFRACTION97
2.4765-2.83460.20391470.15092955X-RAY DIFFRACTION97
2.8346-3.57040.18471480.15252983X-RAY DIFFRACTION96
3.5704-29.9250.17321420.14793001X-RAY DIFFRACTION93

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