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- PDB-7m0h: DHP B in complex with 4-chlorophenol ligand -

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Basic information

Entry
Database: PDB / ID: 7m0h
TitleDHP B in complex with 4-chlorophenol ligand
ComponentsDehaloperoxidase B
KeywordsOXIDOREDUCTASE / peroxidase / peroxygenase / complex
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / peroxidase activity / 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
4-chlorophenol / PROTOPORPHYRIN IX CONTAINING FE / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 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 1.0Aug 31, 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
Revision 1.2Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen

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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)32,5118
Polymers30,8292
Non-polymers1,6826
Water3,315184
1
A: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2564
Polymers15,4141
Non-polymers8413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2564
Polymers15,4141
Non-polymers8413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.580, 67.384, 67.699
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) / Plasmid: pET16b
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: isolated from a genetically manipulated source
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-4CH / 4-chlorophenol


Mass: 128.556 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5ClO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
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: 2.12 Å3/Da / Density % sol: 42.03 %
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: Aug 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. obs: 21635 / % possible obs: 99.6 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 14.6
Reflection shellResolution: 1.92→1.95 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1047 / CC1/2: 0.761 / % possible all: 99.6

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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: 1.91→37.264 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2447 1994 9.24 %
Rwork0.1848 --
obs0.1903 21591 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.91→37.264 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2128 0 112 184 2424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072331
X-RAY DIFFRACTIONf_angle_d0.9163168
X-RAY DIFFRACTIONf_dihedral_angle_d9.8561823
X-RAY DIFFRACTIONf_chiral_restr0.042320
X-RAY DIFFRACTIONf_plane_restr0.004405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.95630.28831290.22511252X-RAY DIFFRACTION91
1.9563-2.00920.2881440.20331385X-RAY DIFFRACTION100
2.0092-2.06840.25741430.19181377X-RAY DIFFRACTION100
2.0684-2.13510.24831370.18391404X-RAY DIFFRACTION100
2.1351-2.21140.25491430.18811391X-RAY DIFFRACTION100
2.2114-2.29990.2561460.19591394X-RAY DIFFRACTION100
2.2999-2.40460.25771370.18991398X-RAY DIFFRACTION100
2.4046-2.53130.22641440.1841385X-RAY DIFFRACTION100
2.5313-2.68990.29681440.19541421X-RAY DIFFRACTION100
2.6899-2.89750.25021430.20371413X-RAY DIFFRACTION100
2.8975-3.1890.261460.1971412X-RAY DIFFRACTION100
3.189-3.65010.2241400.18361421X-RAY DIFFRACTION100
3.6501-4.59740.20621480.15411451X-RAY DIFFRACTION99
4.5974-37.260.23561500.17611493X-RAY DIFFRACTION98

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