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- PDB-4dwu: Carbonmonoxy dehaloperoxidase-hemoglobin A structure at 1.44 Angs... -

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Basic information

Entry
Database: PDB / ID: 4dwu
TitleCarbonmonoxy dehaloperoxidase-hemoglobin A structure at 1.44 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 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
Water3,351186
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.922, 67.622, 68.391
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.: 186 / 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: 42.88 %
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: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.91339 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 14, 2010 / Details: Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Rosenbaum-Rock double crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91339 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.866
11-H, L, K20.134
ReflectionResolution: 1.44→44.2 Å / Num. all: 46314 / Num. obs: 43419 / % possible obs: 93.75 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 24.6
Reflection shellResolution: 1.44→1.482 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 3.2 / Num. unique all: 3356 / % possible all: 57.53

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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→44.2 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.54 / SU ML: 0.056 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.019 / ESU R Free: 0.018 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20224 2353 5.1 %RANDOM
Rwork0.17937 ---
obs0.18059 43419 93.75 %-
all-46314 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.981 Å2
Baniso -1Baniso -2Baniso -3
1--3.78 Å2-0 Å2-0 Å2
2--0.47 Å20 Å2
3---3.3 Å2
Refinement stepCycle: LAST / Resolution: 1.44→44.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2182 0 115 186 2483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193288
X-RAY DIFFRACTIONr_bond_other_d0.0010.022294
X-RAY DIFFRACTIONr_angle_refined_deg2.7431.9934512
X-RAY DIFFRACTIONr_angle_other_deg0.87735607
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9675433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.87224.11163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.43915630
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2661527
X-RAY DIFFRACTIONr_chiral_restr0.0830.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023963
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02752
LS refinement shellResolution: 1.44→1.482 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 116 -
Rwork0.33 1931 -
obs-1931 57.53 %

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