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- PDB-1ew6: THE CRYSTAL STRUCTURE AND AMINO ACID SEQUENCE OF DEHALOPEROXIDASE... -

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Basic information

Entry
Database: PDB / ID: 1ew6
TitleTHE CRYSTAL STRUCTURE AND AMINO ACID SEQUENCE OF DEHALOPEROXIDASE FROM AMPHITRITE ORNATA INDICATE COMMON ANCESTRY WITH GLOBINS
ComponentsDEHALOPEROXIDASE
KeywordsOXIDOREDUCTASE / GLOBIN / HALOPHENOLS
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 / Globins / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Dehaloperoxidase A
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / Resolution: 1.78 Å
AuthorsLebioda, L.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: The crystal structure and amino acid sequence of dehaloperoxidase from Amphitrite ornata indicate common ancestry with globins.
Authors: LaCount, M.W. / Zhang, E. / Chen, Y.P. / Han, K. / Whitton, M.M. / Lincoln, D.E. / Woodin, S.A. / Lebioda, L.
History
DepositionApr 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: DEHALOPEROXIDASE
B: DEHALOPEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5226
Polymers31,0972
Non-polymers1,4254
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.500, 68.400, 61.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DEHALOPEROXIDASE


Mass: 15548.597 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: POLYCHAETE / Source: (natural) Amphitrite ornata (invertebrata) / References: UniProt: Q9NAV8
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 8000, 200 MM AMMONIUM SULFATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 277 K / pH: 6.5 / Details: Zhang, E., (1996) Acta Crystallogr., D52, 1191.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-10 mg/mlprotein1drop
2200 mMammonium sulfate1reservoir
330 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Oct 12, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.78→10 Å / Num. obs: 24637 / Observed criterion σ(F): 3 / Observed criterion σ(I): 1 / Redundancy: 2.3 % / Rmerge(I) obs: 0.051
Reflection
*PLUS
Num. measured all: 66563

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.78→8 Å / σ(F): 3 / σ(I): 1 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.225 2000 RANDOM
Rwork0.197 --
all0.222 30000 -
obs0.207 24637 -
Refinement stepCycle: LAST / Resolution: 1.78→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2192 0 96 107 2395
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.008
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / σ(F): 3 / Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1

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