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- PDB-3lb3: Two-site competitive inhibition in dehaloperoxidase-hemoglobin -

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Basic information

Entry
Database: PDB / ID: 3lb3
TitleTwo-site competitive inhibition in dehaloperoxidase-hemoglobin
ComponentsDehaloperoxidase A
KeywordsOXIDOREDUCTASE / PEROXIDASE / GLOBIN / Heme / Oxygen transport / Transport
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
4-chlorophenol / PROTOPORPHYRIN IX CONTAINING FE / Dehaloperoxidase A
Similarity search - Component
Biological speciesAMPHITRITE ORNATA (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
Authorsde Serrano, V.S. / Franzen, S. / Thompson, M.K. / Davis, M.F. / Nicoletti, F.P. / Howes, B.D. / Smulevich, G.
CitationJournal: Biophys.J. / Year: 2010
Title: Internal binding of halogenated phenols in dehaloperoxidase-hemoglobin inhibits peroxidase function.
Authors: Thompson, M.K. / Davis, M.F. / de Serrano, V. / Nicoletti, F.P. / Howes, B.D. / Smulevich, G. / Franzen, S.
History
DepositionJan 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_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 A
B: Dehaloperoxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8759
Polymers31,0972
Non-polymers1,7787
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-86 kcal/mol
Surface area13270 Å2
MethodPISA
2
A: Dehaloperoxidase A
hetero molecules

B: Dehaloperoxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8759
Polymers31,0972
Non-polymers1,7787
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_544x+1/2,-y-1/2,-z-11
Buried area3530 Å2
ΔGint-85 kcal/mol
Surface area13350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.201, 67.210, 68.724
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
#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-4CH / 4-chlorophenol


Mass: 128.556 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5ClO
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 43.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 0.2 M AMMONIUM SULFATE, 32% 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: 1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 22, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→35 Å / Num. all: 22277 / Num. obs: 21082 / % possible obs: 94.2 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 7.95
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 3.35 / Num. unique all: 1573 / % possible all: 92.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QFK

2qfk


Resolution: 1.85→35 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.914 / SU B: 8.467 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1195 5.4 %RANDOM
Rwork0.187 ---
obs0.19 21082 94.2 %-
all-22277 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20 Å2
2---0.57 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.85→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2182 0 117 213 2512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222788
X-RAY DIFFRACTIONr_angle_refined_deg1.1572.0643865
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0955387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.35124.362149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.08915542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3391524
X-RAY DIFFRACTIONr_chiral_restr0.0840.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022220
X-RAY DIFFRACTIONr_nbd_refined0.1950.21391
X-RAY DIFFRACTIONr_nbtor_refined0.30.21886
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2222
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.2100
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.244
X-RAY DIFFRACTIONr_mcbond_it0.541.51624
X-RAY DIFFRACTIONr_mcangle_it0.85522575
X-RAY DIFFRACTIONr_scbond_it2.10431330
X-RAY DIFFRACTIONr_scangle_it2.0724.51222
X-RAY DIFFRACTIONr_rigid_bond_restr2.29732954
X-RAY DIFFRACTIONr_sphericity_free2.8593213
X-RAY DIFFRACTIONr_sphericity_bonded1.34232671
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 93 -
Rwork0.209 1480 -
obs--92.91 %

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