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- PDB-4dwt: Carbonmonoxy dehaloperoxidase-hemoglobin A structure at 2.05 Angs... -

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Basic information

Entry
Database: PDB / ID: 4dwt
TitleCarbonmonoxy dehaloperoxidase-hemoglobin A structure at 2.05 Angstrom resolution
ComponentsDehaloperoxidase A
KeywordsOXIDOREDUCTASE / peroxidase / globin / hydrogen peroxide / 2 / 4 / 6-trihalophenol
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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Dehaloperoxidase A
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
Authorsde Serrano, V.S. / Zhao, J. / Franzen, S.
CitationJournal: To be Published
Title: A unique role for the distal histidine observed in carbonmonoxy dehaloperoxidase-hemoglobin A structures
Authors: de Serrano, V.S. / Zhao, J. / Franzen, S.
History
DepositionFeb 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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)32,86711
Polymers31,0972
Non-polymers1,7699
Water3,315184
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.910, 67.470, 68.720
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 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, Oxidoreductases; Acting on a peroxide as acceptor
#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-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO
#4: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.16 Å3/Da / Density % sol: 43.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 0.2 M ammonium sulfate, 32% w/v PEG4000, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 22, 2010 / Details: Osmic Confocal X-ray optics
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.05→35 Å / Num. all: 16589 / Num. obs: 16541 / % possible obs: 99.71 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 7.9
Reflection shellResolution: 2.05→2.102 Å / Redundancy: 5 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1171 / % possible all: 98.71

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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: 2.05→35 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.687 / SU ML: 0.124 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23793 877 5 %RANDOM
Rwork0.20007 ---
obs0.20198 16541 99.71 %-
all-16589 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.536 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å2-0 Å2-0 Å2
2--0.14 Å20 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.05→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2182 0 115 184 2481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193288
X-RAY DIFFRACTIONr_angle_refined_deg2.3891.9934512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0045433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.87424.11163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.31715630
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8971527
X-RAY DIFFRACTIONr_chiral_restr0.0860.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022649
LS refinement shellResolution: 2.05→2.102 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 64 -
Rwork0.252 1156 -
obs--98.71 %

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