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- PDB-4fh6: Structure of DHP A in complex with 2,4,6-tribromophenol in 10% DMSO -

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Basic information

Entry
Database: PDB / ID: 4fh6
TitleStructure of DHP A in complex with 2,4,6-tribromophenol in 10% DMSO
ComponentsDehaloperoxidase A
KeywordsOXIDOREDUCTASE / peroxidase / globin
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
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / 2,4,6-TRIBROMOPHENOL / Dehaloperoxidase A
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
Authorsde Serrano, V.S. / Franzen, S.
CitationJournal: Biochemistry / Year: 2013
Title: Structural and Kinetic Study of an Internal Substrate Binding Site in Dehaloperoxidase-Hemoglobin A from Amphitrite ornata.
Authors: Zhao, J. / de Serrano, V. / Zhao, J. / Le, P. / Franzen, S.
History
DepositionJun 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 1.2Apr 24, 2013Group: Database references
Revision 1.3Sep 13, 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,42212
Polymers31,0972
Non-polymers2,32510
Water4,288238
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-83 kcal/mol
Surface area13400 Å2
Unit cell
Length a, b, c (Å)57.634, 67.246, 69.000
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 A


Mass: 15548.597 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amphitrite ornata (invertebrata) / Gene: dhpA / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9NAV8

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Non-polymers , 6 types, 248 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.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TBP / 2,4,6-TRIBROMOPHENOL


Mass: 330.799 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H3Br3O
#5: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.15 Å3/Da / Density % sol: 42.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 0.2 M Ammonium Sulfate, 32% w/v PEG 4000, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.91339 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 14, 2010
Details: Rosenbaum-Rock double-crystal monochromator: sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91339 Å / Relative weight: 1
ReflectionResolution: 1.44→35 Å / Num. all: 46777 / Num. obs: 46300 / % possible obs: 98.98 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 8.2 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 11.9
Reflection shellResolution: 1.44→1.447 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 2.69 / Num. unique all: 3423 / % possible all: 98.61

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QFK

2qfk


Resolution: 1.44→35 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.357 / SU ML: 0.041 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.028 / ESU R Free: 0.019 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The ligand TBP was positioned in the structure by making use of anomalous scattering of bromine atoms to the anomalous difference maps in ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The ligand TBP was positioned in the structure by making use of anomalous scattering of bromine atoms to the anomalous difference maps in order to locate and position bromine atoms of the tribromophenol molecule
RfactorNum. reflection% reflectionSelection details
Rfree0.23329 2454 5 %RANDOM
Rwork0.20312 ---
obs0.20463 46300 98.98 %-
all-46777 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.181 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---1.51 Å2-0 Å2
3---1.63 Å2
Refinement stepCycle: LAST / Resolution: 1.44→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2181 0 129 238 2548
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193203
X-RAY DIFFRACTIONr_bond_other_d0.0010.022199
X-RAY DIFFRACTIONr_angle_refined_deg2.4981.9984411
X-RAY DIFFRACTIONr_angle_other_deg0.85935373
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9995422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.41824.151159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.89315588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4851524
X-RAY DIFFRACTIONr_chiral_restr0.0720.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023900
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02748
X-RAY DIFFRACTIONr_rigid_bond_restr1.63135401
X-RAY DIFFRACTIONr_sphericity_free18.335554
X-RAY DIFFRACTIONr_sphericity_bonded4.25355463
LS refinement shellResolution: 1.44→1.477 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 167 -
Rwork0.365 3375 -
obs-3375 98.61 %

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