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

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Basic information

Entry
Database: PDB / ID: 7lzn
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: 1.95 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

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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
Water2,558142
1
A: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3825
Polymers15,4141
Non-polymers9684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2904
Polymers15,4141
Non-polymers8763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.602, 67.772, 67.554
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, 149 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.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-5JC / 2,4-dichlorophenol


Mass: 163.001 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H4Cl2O
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.21 Å3/Da / Density % sol: 44.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: PEG4000, ammonium sulfate, sodium cacodylate buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 20624 / % possible obs: 99.6 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 15.3
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.481 / Num. unique obs: 1019 / % possible all: 99.8

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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: 1.95→44.756 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.14
RfactorNum. reflection% reflection
Rfree0.2613 1995 9.69 %
Rwork0.1992 --
obs0.2053 20582 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→44.756 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2137 0 120 142 2399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082359
X-RAY DIFFRACTIONf_angle_d0.9743206
X-RAY DIFFRACTIONf_dihedral_angle_d26.309839
X-RAY DIFFRACTIONf_chiral_restr0.044322
X-RAY DIFFRACTIONf_plane_restr0.005409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.99380.28741340.2441278X-RAY DIFFRACTION96
1.9938-2.04770.31771420.22671318X-RAY DIFFRACTION100
2.0477-2.10790.32241360.22251287X-RAY DIFFRACTION100
2.1079-2.1760.26041450.2261318X-RAY DIFFRACTION100
2.176-2.25370.30851410.22741325X-RAY DIFFRACTION100
2.2537-2.3440.33231400.22641299X-RAY DIFFRACTION100
2.344-2.45060.30981410.21071325X-RAY DIFFRACTION100
2.4506-2.57980.29911460.20511328X-RAY DIFFRACTION100
2.5798-2.74140.27861420.21541338X-RAY DIFFRACTION100
2.7414-2.95310.26021410.20861319X-RAY DIFFRACTION100
2.9531-3.25020.29451460.21231345X-RAY DIFFRACTION100
3.2502-3.72030.24191480.19321344X-RAY DIFFRACTION100
3.7203-4.68640.19861450.14891358X-RAY DIFFRACTION100
4.6864-44.7560.20831480.1811405X-RAY DIFFRACTION97

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